i think this is all just pure coincidence. sometime transfers work and sometimes they don't. i doubt your tweaking makes any difference.
as for running firewall just becuase of running ftp server, that's pointless. firewall is designed to block access to a system, but in order for ftpd to work you need to punch holes in your firewall. so you're defeating the purpose of a firewall. seems like you've been infected by GRC virus
keeping your system up to date and having good IDS is the best thing you can do.