I was having the same problems and am still tweaking the settings, but now seem to have no subtitles in MKV files.
I have set the following on the "Transcoding Settings" - "Video Files Engines" - "MEncoder":
Subtitles language priority - off
Audio/subtitles language priority - off;off
Tick Box "ASS/SSA Subtitles" - not ticked
Tick Box "Autoload *.srt/*.sub subtitles....." - not ticked
Not sure if these will cause other problems for me, but at the moment they work.
I've noticed that there is also a "Definately disable subtitles" tick box at the bottom of the "Common transcode settings" page, but I have not had to use that.