I have seen this quite a bit while supporting routers at my last gig at an e-commerce company. A handful of customers would have packet sequence numbers jump, and we would miss a block of data that was the window size of the last good packet.

If you believe Net::Ftp may have something to do with it, try using the Windows FTP client do do the comm. You could even call it from Perl with something like:

`ftp -s scriptfile.txt`;
[download]

scriptfile.txt would contain the open command, the username, password, and everything you would type to the ftp client if you were running it interactively. One command per line, just like a batch file.

But, were I a gambling man, I'd bet money it ends up being hardware.