thats pretty strange. perhaps the zaquencer firmware is larger than the oem firmware and is therefore loaded into a corrupt portion of the eeprom that isnt touched with the oem? thats my best guess.
its not unheard of for these units to have problems with switches, knobs, internal components such as the multiplexer etc etc. i would try to reflash it and then reflash the behringer firmware to verify that your switches work or not. my bet is on your hardware malfunctioning.