Wow! i was just curious about the hdd's.
I'm no expert in this field by any means but i suspect it will be a source code issue.
Also the files themselves may not be converted properly as i'm assuming alot of them are from torrent sources.
The file is only as good as the source.
Mkv files are Matroska codec if you have too many different players and source codecs installed i believe this is creating a conflict.
Here's a good read and i hope it can resolve your issue.http://www.afterdawn.com/guides/archive/how_to_play_mkv.cfm