Thanks for all of the ideas. Comments on each:

@Eliya - Unrelated to the 'or die' portion. It crashed before this, I only added it to try to debug - nothing has ever printed with it. Never heard of Unison but if all of this fails, I'll give that a shot.

@JavaFan - Never heard of rsync either but it also looks promising.

@salva - You're right about rput not failing. I just updated Perl, SSH2, Foreign, and the Backend and no change. I have some output from the code you suggested, I'll send it your way shortly. Some interesting info: I ran it twice after trying to make small changes. While the file size is the exact same and the same number of lines output, the files described are not the same - that I can see of. I hope you can make some sense of it.