Sometimes, if the membrane hasn't been glued down properly, it will be a bit loose in spots or even form bubbles. As long as loose section is intact - no rips or holes - it should be ok. That loose section should still be wrapped around the edge and tucked beneath a gutter and properly sealed where the gutter meets the rubber roof.
Unfortunately, many leaks are not "obvious" and, if not caught early, can cause significant damage - as you have found out.
If you are certain the roof has no leaks, start working your way down the sides checking all the windows, vents and other access areas are located such as the fridge, furnace, storage compartments, speaker mounts, awning support brackets, etc.
Weather and temperatures permitting, try spraying some water on your roof and over your RV and see if you can spot any new signs of water entry.
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2008 Cougar 5th Wheel 27RKS
2005 2500 GMC Duramax
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