What am I missing? Would there be any reason the remaining pump on the RH side had higher output pressure than the LH wing pumps?
When you build a pump, it will have a specified nominal output pressure, and an acceptable "range". If you fit 4 of these identical pumps to an aircraft, by definition, they will all have slightly different output pressures.
As above, the QRH balancing process is clear - you turn off BOTH pumps on the lighter side. You then MONITOR very closely the balance, and do not let it build up. If you just turn off 1 pump, you might as well toss a coin in the air as to which tank will supply the fuel: L, R, or both.