Just for clarity, for anyone who finds this while searching, both XBMC and UnleashX write to the Xbox disk properly, so that's unlikely to be the cause of the problem.
There is a small bug in the UnleashX FTP client, where it will occasionally miss a couple of files it is retrieving from a server if you are using it to pull a large directory from an FTP server. In the opposite direction (pushing files to an FTP server) it works fine, and in both cases the files are written to the disk correctly. However, you weren't using the UnleashX FTP client, you were using XBMC as the client, and XBMC doesn't have that bug. The only other major component is the FTP server on your PC (you don't say which one you were using) so that is almost certainly the source of the problem, and I suspect that flux2k has probably hit the nail on the head - your original PC FTP server was defaulting to sending files as ASCII.