I found a way to work around this using a MEncoder config file.
See the details here http://www.mplayerhq.hu/DOCS/man/en/mplayer.1.html
Apparently you can send a command to MEncoder that will add a time delay, or render a track that does not exist. Effectively disabling the sub titles.
I liked the track selection option... here is how you do it.
Create a text file named "mencoder.conf
" and place it in your "C:\Program Files\MediaCoder-0.7.2.4522\codecs\mplayer
Edit the mencoder.conf file and add this line "sid=31
" to select sub title track 31 (which hopefully does not exist in your MKV video)
Alternately you can delay the subtitle rendering with "subdelay=9000
" which will delay the subs for 9000 seconds... the idea being the delay is longer than the video.
Each method is working for me, however I think the SID=31 is a bit more elegant.
It would be nice if mediacoder could manage these commands for us.
Thanks to the MC team for all the hard work.