I had a similar problem on my beneteau 423. Mine wasn't running all of the time, but when I manually turned it on, it ran but wouldn't pump water. I have strainers in front of the pumps. Cleaned them out and still nothing. I ended up determining that they would pump if the intake was full of water, but they wouldn't self prime. Talked to Jabsco and they said it should self-prime, but if it wouldn't, a pump rebuild might be in order (the boat was 2 years old at the time). I ordered a rebuild kit, and sure enough, that fixed it. The pump would pump water fine, but if the intake was empty, it wouldn't self prime.
The other thing the jabsco rep suggested was that an air leak in the input line might cause the same problem. They didn't like that beneteau used a shared pickup hose for two pumps. (My manual and automatic bilge pump share the same pickup hose)
Hope that helps...
Beneteau 423 #310