This is very perplexing. Your pedal must not have the problem that i thought it might have with the eeprom. I suppose we can try a different micro…although all signs are indicating that you have a good micro controller. If you end up getting a new one i’ll throw in a new crystal to try out too. Speaking of that, are you sure the 22pF clock filter caps are in the correct place, and not 100nF caps?
Are you sure there is nothing shorting anything on the board…like the back of the pots or anything? Something like that would make the most since to me.
Would you mind taking some detailed, focused photos of both sides of your board to see if something sticks out to me? Sometimes it helps with these types of things to have another set of eyes looking at it. You can always email them to me if you can’t figure out a way to post them: info “at” zeppelindesignlabs.com
Sorry for the frustration. We’ll figure this out one way or another.
-Brach