Is the Jabsco pump working correctly? I had a simlar issue with mine, back filling water and it was being supplied (or so I assume) from the waste holding tank, as I had vaccu-sucked it out but ran lots of water back into for flushing.
Found a new replacement pump on Amazon for $45, 3 hose clamps, 6-8 screws later it pumps, fills, drains, and locks like a charm. Apparently they did a change on the check valve seal on newer models and its made a big improvement in performance.
(not to de-rail, but what do you guys use for odor blocking? I tried that dry powder stuff at West Marine, and HOLY COW does it make a difference, not sure how long its good for though)