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I had this problem twice, first time I just sealed the threads on the bolts, then I noticed there is a ridge with a gap around it that the bolt sleeves into. I then re sealed the threads as well as glopped on a bunch around the rest. Check for a thread labeled SEAL YOUR ROOF RACK BOLTS PART 2 for a step by step photo how to as well as lots of other inputs like how overtigtening can actually crack the roof causing leaks from other areas.
