The single extruder has a micro switch on the right side. The dual extruder does not have this micro switch and bangs against the far right stop during the auto leveling procedure. Is this normal?
Mine does this too. Is there room to level a bit closer to the center of the bed? If so, you can download the source for the LulzBot Marlin firmware here, and modify Configuration.h so
RIGHT_PROBE_BED_POSITION
is a couple mm smaller. Compile and download it using Arduino 1.0.6 (note the version). Before you flash it, run M501 to echo back all the EEPROM settings. Write these down, as these will be reset with a FW update. Once you flashed it, set all the parameters to what was in the EEPROM, and then use M500 to store them back in EEPROM.
Note that that firmware is for the regular dual extruder, not the flexydually.