This observation raises a pressing stylistic point: is there a consistent policy about use of the first person plural here at the Lab? Strangely enough, I think there may well be. Although I haven't gone through my archives to check, I suspect that the editorial "we" is reserved for situations in which I'm writing about general editorial policy or technical matters. That is, "we" refers to everything that would be handled by the intern if we had an intern.
Anyway, since I do the programming for the scripts that make the site work, even though we run those scripts, it should be noted that I've been investigating the problem, and it seems to be something ganging aglay with the FTP put command returning success when, in actuality, it has failed utterly; graphical FTP clients aren't doing any better. For now, I'm hand-uploading files using a one-file-at-a-time SFTP client, but this method of doing things isn't tenable in the long run.
I'm looking for a good Windows SFTP client that can be automated well enough to run interactively from Perl. If you know of one, please get in touch.