New or used?
Where do you haver your diverters valves set.
If you are trying to power the seats and the foot jet at the same time then yes you will have less pressure at the seat. Foot jets takes a lot of water from the seats in most spas. Number of jets... if pump 1 is working more jets then pump 2 there might be a slight difference but most spas are balanced out.
Other things that can effect flow: Blockage at the face of the pump, incorrect wiring on the circuit board, partially closed gate/slice valve. Closed or partially closed jets.
If the high speed amp draw is the same on pump 1 as pump 2 then there should be no difference in flow pressure if there is the same amount of jets to each pump and assuming the diverter valves are set in the proper position to send all power to the seat jets.