I assume that clear the EEPROM is M502, M500, is this correct. This does not seem to have changed anything.
I looked through the Configuration.H line by line but couldn't find anything unexpected.
Something that is new, or not noticed before, is that calling Home Z results in homing of X, Y and Z in that order.
For speed, I will start with a new copy of the Repetier firmware, a new Arduino board and a new RAMPS board if I can find one. I will also reconfigure completely instead of using the existing Configuration.H and Pins.H
Mike