I wouldn't call a roof leak a 'working out the kinks' problem. A one-piece rubber roof should not leak except at a rupture or around a faulty pretuberence installation (that's probably spelled wrong but FRF spent all its money on smiley faces and couldn't afford a spellcheck
You stated that all the leaks have been fixed, but you didn't say whether they were all at the same place.
Tracing a water leak source is a b*tch. It sounds like your dealer is on top of things, but for those experiencing this frustrating problem I'd suggest identifying when and where the leak is observed.... Wind and rain direction at the time, etc. Pics of the leak occuring will help the dealer. And eliminate all the last-thing-looked-at items first. Clearance lights are a real culpret, and I've seen a FR trailer with the bottom of the lens caulked but not the top, creating a nice little bathtub to hold the water until it flows in the wiring hole. (the dealer re-lapsealed the roof/side seam and pulled and replaced the front window twice before the one leaking clearance light was noticed.) Roof vents, antennas, dishes, A/C, etc, are all possible leak sites.
Remember, if it gets past the rubber roof membrane, its water on wood.... never a good thing. Working out the kinks associated with a rotted roof deck is a whole different matter!