If I had to guess, I would say your hard drive is the problem b/c it's slow and the file is probably fragmented. Combine those two and the computer has a hard time getting the pieces of the file into VLC fast enough.
I use a program called idefrag to keep my volume with my HD movies all tight and clean. This may turn into a giant defragging debate, so let me preempt that and give you the truth on defragging: Generally not needed, unless you're in a situation like you are (or you're a geek that wants every millisecond of performance)
Before defragging, you may be able to test the theory by burning the file to a DVD (as data) and trying to play off of that, or if you have a 4 or 8 gig ipod nano around, clean out the music and try to play the file off of that.
I guess the first question I should have asked is does it always happen with every HD movie you're watching or just this one, and does it always happen at the same spot in the troublesome movie? If it's the former, then I'm probably wrong, if it's the latter, I'm probably right.
Good luck.
