Something I should correct: I just went back and reread my report, and realized there may be one mistake: the behavior/issue/etc is all accurate, but that FTP log snippet I provided may've actually been when it was recanning the *destination* (as the destination file did show as size 0) rather than the source. Oops, sorry. So I'm not certain if the issue is that it actually shows the source filesize as 0, or that it shows the source filesize as (what it really is), but then when it tries to copy the file, it fails, creates a 0-byte file over the old backup, and reports it succeeded. Make sense?
(Just want to be certain you don't end up chasing ghosts...)
(Just want to be certain you don't end up chasing ghosts...)