The ISP and the router can make a difference.
I had a customer last week who couldn't download a single thing from FTP from HP, yet I could from home. Turned out it was a setting in his router.
Most ISP's have a auto disconnect of connections when it doesnt see anything go through it for a short time. I had this problem with remote desktop. Thankfully remote desktop has a reg key option to send a "heartbeat" packet every few sec. to make sure the connection stays open.
Most FTP programs have an option like that as well. That might do the trick for you.
Shane