Hmm, I wonder if it was the glue along the edges? My trailer is 6-1/2' wide, with a floated filon roof and it looks great 4 years later. The only difference is that I didn't use any glue, anywhere on the roof. Just aluminum insert trim screwed though the filon. Maybe that leaves the filon some room to expand and contract without bunching?

You might try totally floating the roof, especially if you plan to use the insert trim anyways. The trim is dead soft and really easy to work with. I think I had my roof on by myself in a couple of hours. You could try the contact cement if it still bunches when it's totally floated and you wouldn't be out a lot of work.
What a drag that happened!
Bruce