I've never used Net::Telnet::Cisco, so I can't speak from experience, but I suspect you need to newline terminate the things you're printing. For example:

$session->print( "$user\n" );
[download]

That said, a quick look at the documentation indicates that the kind of stuff you're doing can be done more easily with methods created specifically for this (e.g., cmd). It may be worth taking a quick look yourself.

If you plan to spend much time with Perl, you'd do well to learn to Use strict and warnings too, though I doubt that's causing you any trouble here and now.