I am having a similar issue but in my case it is with AVI files. Some of them are recognized but when I try to play them nothing happens. And as far as FLAC, I don't think I can even play them. LMCE won't even see them.
I was wondering if you ever got your problem resolved and what the solution might have been.
Would this be a codecs issue? I am a newbie when it comes to Linux but I am not afraid to fool with it. I have been searching on how to download and install new codecs for Xine and found a couple of articles on how to do this with Ubuntu. I just didn't want to waste my time if nobody thinks this could possibly be the issue.
Looking forward to a reply, in the meantime I will keep searching the forums for an answer.