I just got it back last Saturday. Nope, said the floor was normal, and not rot. They said the soft spots are normal, and did not fix it. Also, when I went down, the repairs on the hitch I took it in for was not done correctly, but they took care of it on the spot. I did get a new door handle, and they repaired the end bunk gasket.
I emailed Jayco support, and they said they would note my problem in the file in case I have trouble out of it later. I doubt that once the warranty is over, they would do anything, but we'll see.
I made the mistake of buying from a dealer 130 miles away, to save a couple grand. I tried taking it to a local Jayco dealer, but since they did not sell the unit, they were not particularly interested in doing warranty work on it.