I wouldn't depend on an FTP server to be nice about connections.. my guess is that you are getting caught waiting for a connection to close. Maybe it will when the other server times out..

Net::FTP is pretty complex but it seems to use sysread (FTP::A/I and sub get in FTP.pm) although it also has many cases to deal with wierd servers and "braindead" firewalls, etc. For example I often see my linux laptop act wierdly when I try to connect to it from a Win98 machine through FTP; it will seem to hang for a long time unless I hit return and maybe still requires me to disconnect and try again (eek). Caveat I am not amazingly experienced at this but it would seem that your control loop depends on well-behaved data streams.