check your settings and make sure its only on 1 connection. mine was set to 2 connections by default so it would try and connect twice to download 2 files at once etc but i found this way it kept timing out. i set it to one connection and it worked flawlessly.
i transfered a 40gb of FF13 from my internal drive to my external drive with the ftp program and it worked fine
now got 40gb of ff13 playing off my external drive
i'm fairly sure this should confirm that you can get games to work on your external if you transfer this way. cause ff13 would not backup onto the external straight from backup manager, but after ripping it to the internal hd, then transfering via ftp to external drive it works fine now.