dont use a USB hub.
increase the VLC file cache (buffer) setting.
if it's a fat based file system on the hard drive is it almost full? if so, it might need to be defragmented.
md5sum the two files to make sure that they are indeed the same to rule out very slim chance that it's a hardware corruption issue.
if all of these don't help, you may want to try a faster spinning external hard drive or changing the interface that the hard drive is using if that's an option.
placing my money on #2 fixing it.
(post is archived)