I now have investigated the problem again and have found that the behavior is due to a bug in mkvmerge. It definitely does nothing have to do with players.
The problem is not limited to the first subtitle (one may get this impression from my first post), but appears with all subtitles (as it seems). The problem seems to appear because mkvmerge does not calculate the duration as you have described in your first reply:
When using timestamp format 2, the timestamps in the timestamp file are ignored in that they do not become the PTS in the MKV file, but are then used to calculate the duration in a wrong way. That’s at least what happened during my tests, if I am not completely mistaken.
I’ll try to file a bug report (hoping that you’re interested in fixing it because mkvmerge does not behave as intended / described).
Thank you very much again, and thanks for the new versions (two updates in two months)!