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Then I suspect you could have an issue with the water pump controller, anytime you have more then one switch they will use one to control the power to the water pump. Click HERE and have a look. That will be between the switches and water pump. Also many times you will have an inline fuse near the pump on the positive wire. I do not know exact location of that controller, if you can not find it I would get a hold of Winnebago they should be able to tell you exact location..... That controller tricks allot of people....
Hope this helps, IF you have more questions or concerns please feel free to contact me... Robert