That's an ugly problem. I have no idea why it might be happening, but if might be useful to know if it's a read problem or a write problem. If you campare the same pair of files several times, do you always get the same answer? If not then it's a problem with reading the files. If you always get the same answer then the error must have occured while writing the copy.

Can you mount the windows disk and try writing a copy to the NTFS partition instead?

You're not out of disk space are you? Try
df -h
and check there's enough space. I think this is probably not the problem because you don't see an out of space error, but it's worth double-checking.