Also check you don't have an airlock in your breather pipe. On my 17.56-2 Expanda I often get issues on the rear tank when I get down to about half full. Water tends to sit in the breather pipe in the low spots as it is such a long pipe going from the filler point near the front through all the crossmembers and around the suspension to the rear. When this happens it tends to suck air down the filler pipe straight into the pump pickup (both tee into the same bung in the bottom of the tank) because of the negative pressure in the tank due to the airlock in the breather. A quick blow down the breather outlet to clear the water and she's all good no more issues.
Had exactly the same problem on our second trip out in the Penguin. Couldn't understand how we could have used 80l of water on the first 3 day trip. The clear refill hose going into the bottom of the tank was empty. WTF!
No other water on board. Borrowed a couple of litres from another camper and then hiked for two hours to bring back 5l of water. I could have driven, but the hike was punishment for not checking and filling the tank. Later that night I tried the manual pump and lo and behold we had water again. Checked the water level on the refill hose and we were almost full.
Problem was that some generous installer at Jayco had routed the breather hose from the top of the tank all the way down under the chassis cross member with plenty to spare. The dealer had filled the tank until water came out of the breather, thus ensuring the breather hose was full of water. The vacuum in the tank was enough to prevent any water coming out of the tank, thus the hand pump just sucked the refill tube dry.
When we got home, I managed to rerun the hose through a cutout in the cross member. It now has only a slight dip which clears easily. I also have a small piece of garden hose to put over the breather outlet to the water out of the breather hose, but after two years we have never needed to use it. We always carry a 10l container of emergency water.
Inspected every new Jayco trailer in the dealer's yard. It was hit or miss as to how the breather hose was run. Some had long loops dangling down, others ran with almost no drop.
It really is a design issue. The inlet and outlet hoses should not come out of a single three-way outlet on the tank.
cheers
Mike