I've just got the Boxee Box, while I've very happy with it in general, it does have a bug where subtitles in MKV files are always displayed.
There is a temporary workaround:
While playing an MKV, open up the video settings and move to the subtitles section way down off the bottom of the screen.
Problem solved!
I hope this helps.. if so, please click on an advert on this site.