Since most 6.5 GB MKV files you could've downloaded are illegal copies of movies, it could simply be a corrupted file. What you can do:
- Try a newer version of VLC.
- Try MPlayer Extended.
- Try Quicktime with Perian.
In my opinion, though, VLC handles MKVs best. It's not about the file size. VLC doesn't load the full file at once into RAM (that would make no sense).