By testing the Latest Snapshot build I noticed that some MKV files still shows embedded subtitles with the GUI option "Definitely disable subtitles" checked.
I found that the MKV files that still show subtitles have setting "Default: Yes", that can be shown with MediaInfo.
I guess that this embedded setting causes that this subtitle somehow is still forced to be used with MEncoder.
Version 1.72.0 works fine where no subtitles are shown with "Definitely disable subtitles" checked.
By testing older snapshot builds I found that Build: d594b2962 (2012-11-20) already has this issue.
MediaInfo text output and debug.log of tested mkv files using Snapshot Build: d594b2962 (2012-11-20):
If I need to provide more info please let me know.