I can use a VMU in either slot with only P1 controller connected. If I connect a controller to P2, the P1 VMU screen dims and it starts beeping every few seconds. It throws an error during gameplay (observed in SoulCalibur) and during any attempt to save. P1 and P2 controllers function as intended and the error(s) vanish when the VMU is removed (although I can't save without one).
If I unplug P2, I can save and play all I want. I don't see any obvious issues with the controller ports/board. Everything checks out with my multimeter. I'd like to rock some SoulCalibur with my friends, but I'm pulling my hair out trying to figure this issue out.