From what's been said - if everything else has been changed, it's probably what NOT been changed that's the problem. Check the wiring, put a voltmeter on the supply, and see what happens!!
For example, if the pumps are wired to battery 1 for bilging when the isolators are off, when you run on battery 1, everything is OK. If you run on battery 2, you might be running the pumps at 24v, which won't go down too well. Or they've used crap wire - and they aren't getting enough oooomph to do the job, and after a couple of weeks give up the ghost.
It all depends on how the system was set up at the beginning - but I'd put money on the supply being the problem.