You know reading threads like this really reaffirm my decision back when I ordered my unit not to go with a skylight. I've heard all too many tales like this and I was really torn as I thought the light it let in would be great, but I just didn't want the hassles as described in this thread.
I believe Andy from Inland RV had a skylight that is made of a bit thicker material. I would check with Inland to see if they are still avail. Good luck with your project.