There is no such thing as a water controller. Only the water inlet valve which turns the flow on & off in response to the signal from the main controller board. The inlet valve must be working ok because you say it does the fill & wash cycle ok. When you say the 2nd stage of the rinse do you mean the deep rinse? What exactly happens at that time? Can you hear the water filling the bowl, is it sounding like a normal flow & has it stopped filling when the beeping starts or is it still in the process? Also, watch the outlet pipe & see if any water is escaping to the drain. This will make it a longer than normal fill time which may trigger a fault condition.
Lincoln Appliance NZ
August 2009