Check to see if the electronic control unit is up side down, or the connections are on the bottom instead of the top. The original units had the connections on the top and water would get in. The unit is on the back, inside. There is also a toggle switch there that changes the cycle.
Second, the toilet needs full voltage to operate correctly. Discharged batteries can cause it to stop half way thru the cycle.
Holiday Rambler Navigator DP, Hummer, and Honda VT1100C Shadow