I had the same thing happen today, after a month with no noise at all. It was a very load and annoying squeak! I noticed there was some dust on the rubber seal. I cleaned it and the squeak disappeared.
My Bronco is 1 week old and I would also like to find an alternative to mud flaps. I have a Wildtrak and it's been raining so I can see the potential for damage to the paint. I do not like the looks of mud flaps and I'm not really to excited about putting a film on the side doors and quarter...