I had the same problem in my 2008 Winnebago Destination. Fortunately it was under warranty. The dealer pulled the interior trim off and you could see the rusted area. They called a body man to the shop and I was fortunate enough to be there when he was there inspecting it.
He said that Winnebago was notorious for this type of leak. That he would fix it and as long as he is alive he would warranty it. So, it is a matter for a good body shop. They will need to grind, prime, fill, and paint the upper area that the window seals against. Once rust forms, it pushes the seal away and the leaks start as a trickle.
Wayne MSGT USMC (Ret) & Earlene (CinCHouse)
2008 Winnebago Destination 39W
It is what it is, and then it is what you make of it.