Went and picked up the trailer today.
They actually performed a pressure test and found all leaks occurring at this time. One was the obvious one by the master bed passenger side; the tech found that the "foam" gasket Jayco uses had been nicked at two corners when installed and was allowing water past it. He also found that the window on the other side of the bed had the exact same problem but only on one corner... he said he sent a photo to Jayco and they told him to pull the window and reset it. So... two windows pulled and new, thick butyl tape put behind them instead of the original foam gasket material. I'm LIKING this so far
The other leak which was coming through the roof and into the wardrobe next to the bed on driver's side was because of air pockets in the lap sealant from the factory. When I was up there cleaning the roof after picking it up from the dealer (see my other thread / rant about that one) I noticed that there seemed like a few big "holes" in the sealant... especially around three of the screw heads. The tech told me that is exactly where he found the leaks. He resealed the whole front seam. I went up and looked at it and it looks waaay better than from the factory as far as coverage.
He also inspected and touched up around the antenna's because they weren't done very well at the factory either... he said it is better to do it right while it isn't leaking yet.
General feelings? I am happy with the performance of this tech crew at this point. The service manager came over and talked with me and told me that in his 30 years, he can remember less than 15 or so Jayco's that have leaked right off the assembly line. I informed him that all wouldn't be right in the world if MINE didn't have problems.
At this point, this is the end to this saga... unless of course the next time it rains I end up with wet places around the inside of my trailer again.
Thank you all for the advice along the way!