If you're sure it's not related to the rim or tire hitting...

What about bearings/chain-to-cassette issues?

Or...this is perhaps the STUPIDEST thing I've ever had go wrong on my bike...my rear reflector got loose and would knock against the rear forks, it was unbeliveably hard to locate for two reasons

A. I never in a million years thought to check the reflector.

B. It would hit, I would look, but it had just been knocked back into place so there wasn't anything to see until just before it would hit again. It only fell out of place in the last 45-30 degress of rotation.