The 3-pin cable that was packaged with the pumps, I believe... I have tried several different configurations. From the pump to the mobo, from the pump to a different mobo, connected to the powered on Aquearo 6... All while connected to power vie the molex.
So, the pumps should power one when connected to power via the molex? Yep, they're definitely not doing that.
The molex power connector should be connected to the PSU.
The 3-pin cable is the included aquabus cable. It connects between the pump's aquabus port and the aquaero;s aquabus high port.
You only need the aquabus connection if you want to control the pump with the aquaero.
If you have two pumps you will need to Y them into the aquaero's aquabus high port using a splitter cable.
If that scenario doesn't work, the symptom you described in the OP appear to have been recognized by the company rep, and you should
follow his instructions.