This is where FTP, and especially the Perl module
Net::FTP, come in. We try to keep it locked down, configured at the firewall so that only the server can FTP into the instrument and even then can only move instrument->server, not the other way around.
One specific machine was set up with Windows 2000 and the FileZilla FTP server. The software, we were told, wanted 2K, and so we ran with that. FileZilla was about the first Google result I hit when I searched on "windows ftp server", and I cannot say there was ever a point where I regretted using FileZilla for all my FTP needs.
Then there was a necessary upgrade that needed Windows XP. The machine had 2 HDs in it, so I installed XP on disc 2 and made it dual boot. And, since it was XP Pro, I had IIS already. I may have had it on the 2K, I never thought to check. Anyway, the machine now spends most of the time under XP. I have had to change the upload-and-munge script to handle the new, and I'm not sure how much is IIS-vs-FileZilla and how much is Instrument-Software 1.3 vs Instrument-Software 2.0.
Where the story threatens to become interesting is this: The person who runs on that instrument, she makes a CSV config. Normally, she copys it, changes it, and seemingly, as long as the Excel file was open, it wouldn't upload. This was the 2K and FZ behavior.
Windows XP and IIS, it seems, FTP anyway, no matter if the Excel file is still open. And I had to clean up after it because of it. Not a problem, to be sure, but something to be aware of.