This is the very reason that I thoroughly read through my insurance policy to know what is covered and what isn't. Also another reason that I am very meticulous about maintenance, both scheduled and routine preventive.
The old cliche when it comes to RV's "water is not our friend" certainly holds true. If there is an opening, water will find it and invade. When water comes in, it will make its presence known in the strangest of places and often far from the actual entry point.
This is certainly not a good experience for the OP, but at the same time I understand why the issue may not be covered by insurance or extended warranty. I hope all ends well.