Lots of variables. I would first get a temp gauge to check the temps of the outlet air, when using the discharge out the bottom of the unit. Don't let it go through the overhead ducts. If there is a difference, set the higher temp unit to a lower temp until you get about the same discharge air temps out of both units. If this can be done, wait a while and see if temps equalize, more or less, in the 2 zones/rooms.
You didn't say which zone got colder, I'll bet the bedroom? Much less area to cool. I just set the thermostats to whatever number is needed to get the room to the temp that I want. Could not care less if they match numbers; unless one is set at the lowest setting and the other near the highest to get the same discharge air temps.
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2018 DX3 37RB - 2017 Jeep GC Summit towed
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