The only thing that seems to remain common is the OS. Have you tried XP? I say that because empirically, I've found that firewire on Vista, and disappointingly, on Win7RC, is flakey. I've been trying to use firewire with external hard drives on both Vista and 7RC and the results are the same so far-terrible performance. As usual, XP does not experience these performance problems (mostly write speed related).
So from that experience so far, I'd want to try anything firewire-related on an XP system for a while and see if the problem went away or was still there before looking further.