Set Track Enabled flag always to Yes?

Thanks for the reply. I deleted my mkvtoolnix-gui.ini file and tried it again. It’s the same. If my input file is a MP4 file which has these two audio tracks:

Summary from MPC-HC
Audio #1
ID                             : 2
Format                         : AAC LC
Format/Info                    : Advanced Audio Codec Low Complexity
Codec ID                       : mp4a-40-2
Duration                       : 49 min 25 s
Bit rate mode                  : Constant
Bit rate                       : 128 kb/s
Channel(s)                     : 2 channels
Channel layout                 : L R
Sampling rate                  : 44.1 kHz
Frame rate                     : 43.066 FPS (1024 SPF)
Compression mode               : Lossy
Stream size                    : 45.2 MiB (3%)
Title                          : Japanese / Japanese
Language                       : Japanese
Default                        : Yes
Alternate group                : 1
Encoded date                   : 2024-02-28 21:51:35 UTC
Tagged date                    : 2024-02-28 21:51:35 UTC
Menus                          : 6

Audio #2
ID                             : 3
Format                         : AAC LC
Format/Info                    : Advanced Audio Codec Low Complexity
Codec ID                       : mp4a-40-2
Duration                       : 49 min 25 s
Bit rate mode                  : Constant
Bit rate                       : 128 kb/s
Channel(s)                     : 2 channels
Channel layout                 : L R
Sampling rate                  : 44.1 kHz
Frame rate                     : 43.066 FPS (1024 SPF)
Compression mode               : Lossy
Stream size                    : 45.2 MiB (3%)
Title                          : German / German
Language                       : German
Default                        : No
Alternate group                : 1
Encoded date                   : 2024-02-28 21:51:35 UTC
Tagged date                    : 2024-02-28 21:51:35 UTC
Menus                          : 6
Summary from ffprobe
{
    "streams": [
        {
            "index": 0,
            "codec_name": "hevc",
            "codec_long_name": "H.265 / HEVC (High Efficiency Video Coding)",
            "profile": "Main",
            "codec_type": "video",
            "codec_tag_string": "hvc1",
            "codec_tag": "0x31637668",
            "width": 1920,
            "height": 1080,
            "coded_width": 1920,
            "coded_height": 1088,
            "closed_captions": 0,
            "film_grain": 0,
            "has_b_frames": 0,
            "sample_aspect_ratio": "1:1",
            "display_aspect_ratio": "16:9",
            "pix_fmt": "yuv420p",
            "level": 120,
            "color_range": "tv",
            "color_space": "bt709",
            "color_transfer": "bt709",
            "color_primaries": "bt709",
            "chroma_location": "left",
            "refs": 1,
            "id": "0x1",
            "r_frame_rate": "24000/1001",
            "avg_frame_rate": "533197500/22238779",
            "time_base": "1/90000",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 266865348,
            "duration": "2965.170533",
            "bit_rate": "4073834",
            "nb_frames": "71093",
            "extradata_size": 126,
            "disposition": {
                "default": 1,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 0,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "und",
                "handler_name": "VideoHandler",
                "vendor_id": "[0][0][0][0]"
            }
        },
        {
            "index": 1,
            "codec_name": "aac",
            "codec_long_name": "AAC (Advanced Audio Coding)",
            "profile": "LC",
            "codec_type": "audio",
            "codec_tag_string": "mp4a",
            "codec_tag": "0x6134706d",
            "sample_fmt": "fltp",
            "sample_rate": "44100",
            "channels": 2,
            "channel_layout": "stereo",
            "bits_per_sample": 0,
            "initial_padding": 0,
            "id": "0x2",
            "r_frame_rate": "0/0",
            "avg_frame_rate": "0/0",
            "time_base": "1/44100",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 130766848,
            "duration": "2965.234649",
            "bit_rate": "128000",
            "nb_frames": "127702",
            "extradata_size": 2,
            "disposition": {
                "default": 1,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 0,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "jpn",
                "handler_name": "Japanese",
                "vendor_id": "[0][0][0][0]"
            }
        },
        {
            "index": 2,
            "codec_name": "aac",
            "codec_long_name": "AAC (Advanced Audio Coding)",
            "profile": "LC",
            "codec_type": "audio",
            "codec_tag_string": "mp4a",
            "codec_tag": "0x6134706d",
            "sample_fmt": "fltp",
            "sample_rate": "44100",
            "channels": 2,
            "channel_layout": "stereo",
            "bits_per_sample": 0,
            "initial_padding": 0,
            "id": "0x3",
            "r_frame_rate": "0/0",
            "avg_frame_rate": "0/0",
            "time_base": "1/44100",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 130763776,
            "duration": "2965.164989",
            "bit_rate": "128000",
            "nb_frames": "127699",
            "extradata_size": 2,
            "disposition": {
                "default": 0,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 0,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "deu",
                "handler_name": "German",
                "vendor_id": "[0][0][0][0]"
            }
        },
        {
            "index": 3,
            "codec_name": "mov_text",
            "codec_long_name": "MOV text",
            "codec_type": "subtitle",
            "codec_tag_string": "tx3g",
            "codec_tag": "0x67337874",
            "width": 1920,
            "height": 162,
            "id": "0x4",
            "r_frame_rate": "0/0",
            "avg_frame_rate": "0/0",
            "time_base": "1/90000",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 266857290,
            "duration": "2965.081000",
            "bit_rate": "125",
            "nb_frames": "985",
            "extradata_size": 68,
            "disposition": {
                "default": 1,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 1,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "deu",
                "handler_name": "German [Full]"
            }
        },
        {
            "index": 4,
            "codec_name": "mov_text",
            "codec_long_name": "MOV text",
            "codec_type": "subtitle",
            "codec_tag_string": "tx3g",
            "codec_tag": "0x67337874",
            "width": 1920,
            "height": 162,
            "id": "0x5",
            "r_frame_rate": "0/0",
            "avg_frame_rate": "0/0",
            "time_base": "1/90000",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 266857290,
            "duration": "2965.081000",
            "bit_rate": "6",
            "nb_frames": "84",
            "extradata_size": 68,
            "disposition": {
                "default": 0,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 0,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "deu",
                "handler_name": "German [Forced]"
            }
        },
        {
            "index": 5,
            "codec_name": "bin_data",
            "codec_long_name": "binary data",
            "codec_type": "data",
            "codec_tag_string": "text",
            "codec_tag": "0x74786574",
            "id": "0x6",
            "r_frame_rate": "0/0",
            "avg_frame_rate": "0/0",
            "time_base": "1/1000",
            "start_pts": 0,
            "start_time": "0.000000",
            "duration_ts": 2965171,
            "duration": "2965.171000",
            "nb_frames": "3",
            "extradata_size": 43,
            "disposition": {
                "default": 0,
                "dub": 0,
                "original": 0,
                "comment": 0,
                "lyrics": 0,
                "karaoke": 0,
                "forced": 0,
                "hearing_impaired": 0,
                "visual_impaired": 0,
                "clean_effects": 0,
                "attached_pic": 0,
                "timed_thumbnails": 0,
                "non_diegetic": 0,
                "captions": 0,
                "descriptions": 0,
                "metadata": 0,
                "dependent": 0,
                "still_image": 0
            },
            "tags": {
                "creation_time": "2024-02-28T21:51:35.000000Z",
                "language": "eng",
                "handler_name": "SubtitleHandler"
            }
        }
    ],
    "format": {
        "filename": "replaced.mp4",
        "nb_streams": 6,
        "nb_programs": 0,
        "format_name": "mov,mp4,m4a,3gp,3g2,mj2",
        "format_long_name": "QuickTime / MOV",
        "start_time": "0.000000",
        "duration": "2965.234649",
        "size": "1607805666",
        "bit_rate": "4337749",
        "probe_score": 100,
        "tags": {
            "major_brand": "mp42",
            "minor_version": "512",
            "compatible_brands": "mp42iso2mp41",
            "creation_time": "2024-02-28T21:51:35.000000Z",
            "encoder": "HandBrake 1.7.3 2024021000"
        }
    }
}

Both audio tracks get the Default track flag set to Yes and the first track has Track enabled = Yes and the second has No.

Am I wrong or are these flags not really what’s set inside the input file and not what you said is the “default settings”.