Crazy timing, I just answered this one on another post! Please see here: Need a smooth first layer / e-step and z offset woes (Regarding too close to bed)
Be sure when installing the new 3.6.3 you clear you cache. We had to make changes to the start gcode to correspond with updated firmware. If you missed clearing the cache, it could be using old start gcode causing some conflicts. If that is not the case, can you reach out to support@lulzbot.com with a quick video showing the issue?