I've got heater problems here too. Bought my 2010 JKU back in the fall and noticed a leak from radiator and "stop leak" all in the radiator. My local shop recommended replacing the radiator before it caused other problems. So I did. That was in the fall, so I wasn't using heat much. Now that its been cold as heck here in Ohio, I've noticed other issues with the heating system. I get cold air from my driver side vent, and hot/warm air from the other vents.
From what I've read on here, sounds like I have a heater core or blend door problem, neither of which is an easy fix.
Anyone have any suggestions on a mechanic/shop that can look into this or fix for less than the dealer. Dealer told me I'm out of warranty (50k miles) and I'm looking at over $1k to take dash off to replace heater core, etc. Ugh!