your company cannot patent/copyright the whole thing, only the code you wrote can be copyright. the part you pinched, that is Net::FTP code, must be excluded from any such proprietary patent/copyright, and the GPL disclaimer must be included (not stripped) from Net::FTP. In other words: you can't take it and put a copyright on GPL (OpenSource) software. My company uses (for Windows install) Cygwin, Perl, etc., but charges for the "system" and maintenance etc. The whole of the "system" (including proprietary binaries) is very flexible and open, but pretty useless to someone who doesn't have all the documentation on how it all works together and how to customize it well.
By the way, careful on your implementation of "recursive FTP". i hope the ftp connection itself (inside a recursive loop) doesn't break the whole chain when one connection in the chain hangs etc.