Try mixing up the order in which the files are sent. If the disk is running out of space during the transfer, you'll get inodes for each file, but no data getting stored for the inodes to refer to -- hence, 0-byte files. If you change the order, and different files are zeroed out, then your server is probably filling up halfway through.
If you change the order of transfer, and the same files are showing up with zero bytes, then Michael Southwell is probably on the right track, with weird stuff in the beginning of your file. -c
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