I'm pretty sure that's a known problem with Amithlon but I'm not sure why it only happens with some PCI devices.
ArakAttack includes a reset command that resets cards that it is aware of to avoid this. This is also mentioned in the ArakAttack help file.
I can't tell you how it works off the top of my head, but I'm pretty sure it's calling something on the x86 side of Amithlon.
I'd disassemble his reset command or try to contact him to see what's going on.