What's your OS, CPU, and Video card specs. This has a direct relation most times.
What's the MKV file specs? Install
MediaInfo and post the tree report on the file that creates this issue. We need this to see how the subs are built into the file, which is most likely the reason for the subs looking like they do on boxee. Unfortunately, Boxee does not support every subtitle format or every MKV encoding option.
XBMC is not related to Boxee and most issues are not related between the two any longer....
Bookmarks