On the other hand, the skylight is a large, unsupported hole and the roof would tend to flex a bit more than other areas.
Assuming you have an inner skylight, if you remove it you'll be able to tell if there's any water incursion. While you're at it, if the inner skylight screws aren't stainless steel, replace them with stainless steel along with any trim washers. They will rust over time.
Mine did have a leak and I was able to pull out some pieces of rotted luan plywood and replace them with some new pieces covered with some waterproof spray adhesive (3m or Gorilla?), but not the contact adhesive type that requires spraying both parts.
2002 Itasca Suncruiser 35U