Roof
Be sure to have your dealer look at them. They can look at it and determine whether or not their are any decking screws trying to work their way up - or more probable - that the liquid glue that was used on the roof has "gummed up" in areas. The glue has a tendency to clot up and form chunks at times. It doesn't pose any threat to breaking through the strong rubber - but if it every did, obviously, we would take care of the repair under warranty.
ST
It looks like they will puncture the rubber. Certainly if they were stepped on they would come through. What now?
