Chukar Hunter, I'll add a couple thoughts along with longhorn.
Sometimes in a house roof, a leak might occur at, say, a roof vent, but might travel some distance on a rafter to find the lowest point to drip from. The aluminum runners in the FWC roof, are slightly arched, front to back, so if you have a leak at a screw hole, or a vent, it might just travel to some other point some distance away, and not necessarily drip straight down.
When I was stripping my roof and prepping it to paint, I removed all the screws. I noticed that most of the screws had been covered with a glob of silicone, but some of the globs were not completely bonded all around the screw. Certainly with time any sealant might loose its grip, and allow water through.
I personally would avoid using any old silicone from the hardware store to reseal screws and trim, and would rather get some of the camper specific products from an rv store, as they remain flexible in all weather conditions, and are often designed to stick in less than ideal conditions.
Close inspection around any vents for sealant cracks, or screws not completely covered with sealant might also be prudent.
Lastly, if your screws don't have neoprene bonded washers on them, you might consider that as well for one more possible way to get a tight seal on the fasteners, along with sealant on top of the screws and washers. You can get these at places like Lowes, HD, or Ace Hardware.
Good luck, it certainly can be frustrating!
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