Have you tried to open it with QuickTime once you have Perian 1.1 installed?, maybe closing the movie while saving changes could merge both… I can't give it a try, for some weird reason I can't see subtitles within QT even with Perian 1.1 installed… I have read than deleting some files from /Library/QuickTime would help to get subtitles back, albeit I haven't had them ever on QT, I have to rely on VLC to use .srt files…