from what specs i found online, you have a 44 gal fresh tank cap, and a whopping 16 gal water heater ???
that is almost half your total water cap right there.
so after you fill your tank, and the first time you turn on your water pump does it run for a while? my theory is you are putting the majority of the water in your water heater tank.
Id turn on your pump (to charge your system and top off the water heater) when your tank is at least half full and then continue filling your tank to top her off.
also, i plan on doing this to get some extra water;
RV.Net Open Roads Forum: 2010 Rockwood Roo 23SS Flat Pancake Water Tank
this mod would allow you to use that extra 10-15 gals
and remember, just because you have 16 gals of hot water but an "empty" water tank, the pump will not have any water to push (either to your water heater or next open water source, toilet, sink etc.)