My JB3 does similar things. I formatted my HD last year, but before that, I was using my firewire card to transfer everything. After the reintall, I go straight for the firewire and on every transfer of more than a few seconds, it stops. So being frustrated, I decided to use the USB port, just for shits and giggles. Lo and Behold, it fucking works! Very strange.
Before the reformat, I had started with USB, and then upgraded to firewire after I got my firewire card. Thus I had originally used the USB port and then switched to Firewire. Now I do vice versa, same setup, same files, and it takes a shit.