Annoyingly, the default setting for playing .mkv files on XBMC is to show the subtitles. It's easy enough to turn this off from within the on-screen display launched with the "m" key while the video is playing. Unfortunately there's a bug in the latest 9.04 release for 64bit Ubuntu which causes the audio configuration dialog to crash when you try to bring it up, so you can't use this to disable subtitles.

This has been fixed in the svn builds, but what do you do if you can't or won't install the unstable release?

Open the configuration file ".xbmc/userdata/guisettings.xml" in gedit and search for "showsubtitles". Following this on the line will be the word "True", so change this to "False", then save and restart XBMC and subtitles should now be disabled by default.

Note: Videos that have already been watched with subtitles showing will not be affected by changing the default setting. It's only new videos that are added to XBMC that will take the default.