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Stock JK TechBulletin board forum regarding issues with OE (original equipment) components of the Jeep JK Wrangler (Rubicon, Sahara, Unlimited and X) such as factory suspension parts, engine, transmission, body parts, interior fixtures and the on-board computer.
A friend of mine has weird noises like you describe in his 2012. Dealer had it for a few days and determined it was the PCV system. They replaced that and all is good.