Try:
http://www.datahidrolik.com/EN-En/ou...%20Systems.asp or use just the name.com and go to Downloads.
Draw your system.
1. Which autopilot? Does it have NRV? Isolate it from the system and test.
2. When turning a helm pump, it first selects a port to feed, and second, as fluid enters the NRV, opens both the feed and return ports. It has a O ringed piston inside sliding to open ports. It seems your pump/porting is slow to pressurize...sugesting, besides air, a leaking valve, piston, or port.
3. If both pumps "slip" one might assume it's not the pumps, but it could be one affecting both. Strange, but the 2 pump diagrams show the ball in the NRVs in a different position....one is wrong.
4. Something simple could be the problem...such as the cly. mount plate bolts.
Cap off auto pilot first (at the T fitting). Then a helm pump. Test one pump or section at a time.