Are the cracks on the roof membrane or is it the caulking around the vents, etc? My roof is heading to ten years and after washing it 3-4 times a year and adding self leveling caulk around the anything that comes through the roof.
Silicone caulk is not the best tool in the tool box when it comes to maintaining your roof. I suspect that it is not compatable with roof membrane. The correct product to use on your rubber roof, even for emergency repairs is a self leveling caulk specificaly for a rubber roof. In a pinch I would use aluminum duct tape to cover the crack or tear.
Go to the Dicor website, they have a bunch of DIY videos on the care and maintenance of a rubber roof.
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