Work with the dealer, he must coordinate the repair with Keystone to get paid, so they will be aware of the issues. If, however, you have problems with the dealer, then it might be appropriate to elevate the problem to Keystone Customer Service.
As for the weatherseal folding over, it should fold out when the slide is extended and fold in when the slide is retracted. There are additional bulb seals inside and outside (on the slide flange) that sit against flat surfaces on the trailer sidewall to help seal when it's in and when it's out.
I'm just guessing here, but the problem may have been causeed by a multiple set of issues. First, as you've noticed, the rain gutter allowed a leak to run down the sidewall of the trailer, dumping water on the slide seal. This is most likely the root of the problem. And, also, "if" your slide was not sitting level (ie: your trailer was slightly high on the slide side) the roof would have possibly allowed water to run "into" rather than "away from" the slide seal.
The slide roof is almost level, there's very little rise to keep water away from the trailer, so being slightly unlevel is often an issue. Many of us (me included) level our RV slightly high on the slide side so when the slide is extended, the RV sits "more level" if we "misjudge" slightly, and that side of the trailer remains slightly high, then it's possible for water to pool on the roof and run back toward the seal. Once water gets to the end of the seal, there's a small gap where it can enter the trailer if the seal doesn't completley "fold over" like it's supposed to.
I'd suggest that you let the dealer look at it, follow his recommendations (if they seem reasonable), get it repaired and keep your slide seals lubricated and make sure they fold over properly. Hopefully, that will be enough to resolve the problem, but keep an eye on it, you only have 2 months of warranty left