I thought I read somewhere that since the risers are extensions of the motherboard it may be safer to run them from the same PSU that powers the motherboard. I've also read not to cross the power like shubaduba suggested. This is why I'm at a loss.
Risers do not transfer any power through USB cable from motherboard. All pins are used for data transfer. So "risers are extensions of the motherboard" only partially, not in case of power delivery.
I did fry a mother board before. I had 2 Risers and 2 GPUs on the first PSU and 3 risers and 3 GPU's on the second PSU. The system was not shutting down properly, the second PSU would not shut down and would somehow kick the first PSU back on and start everything up. I had the system shut off and plugged a Riser into the mother board and the power discharging started the whole rig up and fried the mobo so I'm paranoid.
Can you show which type of PSU-to-PSU synchronizer is installed?
You can try to swap PSUs. Some of them do not like being slave.
Risers do not respond for proper PSU power up/down.
I have never encountered such problems with any of 8 rigs I have built.
It is not recommended to connect directly into motherboard PCIex port, because GPUs will draw much power from MB.
I thought you have no enough risers.
But if you have, then 3 + 2 as you described would be perfect power balanced scheme.
To avoid ground/static burnouts it is highly advised to connect both PSUs cases with any 18+ AWS cable