I'm in the middle of a saga with this myself. I have a 2014 R/T with auto leveling lights. I had the passenger side assembly replaced under warranty and they never reset the computer so both headlights were pointing literally at the ground in front of the car (not fun driving up an unlit parkway at 430 in the morning going to work). So I brought it back and they reset the computer but the assembly they replaced was still too low even though the system was now working properly. I brought it back again, they reset it again and no change. So I opened a case with FCA and brought it to another dealer. They told me they deactivated the auto level system, then manually zeroed out the lights, then reactivated the auto level system and now the headlight which was replaced is about 3" higher than it was against the shop wall and even with the other light. I haven't had the car out at night but it sounds like this second dealer actually knows what they are doing and did it the right way. So my guess is your dealer doesn't know what they are doing and you should find one who does.
