Dave, it's likely you have not only a luan wood roof substrate below the rubberized roof cover, but also a layer of 'styrofoam' rigid roof insulation layer below the luan that provides for some roof movement, temperature changes, and gives the ability to more easily walk on the roof without the luan being stressed as much between aluminum roof joists, which is why your length of screw may not have quite reached the joist.
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the Turners...
two Campers, two Electric cars
former diesel pusher traveler
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