I agree with spotco2 about galvanic corrosion being the issue. The best bet to stopping it permanently would be to find someone who can sandblast or more preferably glass bead the hinges till all corrosion is removed and the part is bare aluminum. Glass bead will leave a smoother less aggressive finish. You will then need to use a quality acid etch primer, primer sealer, and then paint all surfaces of the hinge. Bedline over the paint if you still want but don't use bedliner as a paint. If you really wanted to go crazy (which you don't I am sure) once the hinges are bare aluminum you could have the them Chromated which is a chemical finish that protects the part from oxidation and corrosion and replaces the need for an etch primer. It is an excellent surface to adhere a primer/sealer and paint to. Chromate is a fairly inexpensive process usually done by any company whom anodizes aluminum. I can have a set of hinges done locally for $15 - $20 bucks. Anytime we have to paint aluminum (I run a company that builds pharma machinery) we have it Chromated first and we have zero peeling issues after painting.Just bought a 2007 JKU with the door hinges paint all bubbled up. What is the best way to remove all the paint and corrosion? I am hoping to use a bed liner type product to coat them, will this keep the bubbling from coming back?
Jeep has released revised hinges that include pads underneath that prevent direct contact between the dissimilar metals. As far as I know these pads are part of the new hinges and are not available separately, but perhaps there's some aftermarket source for similar pads....I believe there is an insulating pad that you can put between the door and hinge when replacing that is supposed to fix the problem but it is questionable if it works.