It is possible when two controllers run of one battery that one of the pumps is set slightly differently or that the motor is less efficient. There are a host of reasons why one pump may take a higher current draw when compared to another.
I am interested in why one controller would show a lower voltage than the other when they are both connected to the same battery. One possible cause of this could be voltage drop along the cable, are one set of leads longer than the other?
Copper while being a good conductor is not 100% efficient as a result there is some resistance to current, so the longer the cable the greater the volt drop along its length
It may also be worth checking for any worn or corroded connectors.
Hi Ian, thanks for you inout(sorry for hi-jacking ya post H20) one of the wires is indeed longer but the longer controller is the one holding charge longer
And I've checked a re-wired both controller and can't seem to see any wear of any sort, so no obvious reason I can see 
Hi I would suggest then that it is the pump motor on one side is not as efficient as the other to be honest it is not something you would even notice running just one pump.
You could even buy two exact same pumps at the same time and there would still be a marginal difference in current draw from the battery. The controllers do not draw much current at all some where in the 100th of an amp range just enough to power the micro processor.
To be honest it sounds like you have covered pretty much every thing else my only other suggestion would be separate batteries one for each pump but to be honest that would be over kill.
Two pumps will run the battery down a little faster and other than the difference in efficiency of the pumps motors you would expect to see the pumps draw much the same current on each.