Well you can never have too much data or too many thermometers so if you're close to an Ikea I'd pick up a couple more of their $8 "Fantast" thermometers. Plus I'd rig up a test experiment with paper clamps and clothes pins to put all your probe tips in a pot of water on the stove and bring it to boil. When the water is boiling vigorously, they should all be reading 212F.
You said you also took ambient air measurements that confirmed a 30-40F temperature variation from top to bottom? They seem to confirm your top is too cool. Any reason to doubt those readings? Were they taken midway between the meat and the wall? And not right after opening the door? Also I don't think you said, but was the cooler piece of meat also the bigger piece of meat? It's always going to take longer, at the same temp, to cook the heavier piece of meat. Although the elevated ambient temperature is what's cooking the meat, the meat is also what's "cooling" the ambient temperature, so the bigger, cooler piece could be playing a role there.
Also most propane vertical chest smokers are not well insulated--the idea is you have plenty of BTUs in that bottle to not worry about insulation! But in cold weather, you're losing a lot of heat through those walls so that can make the bottom significantly hotter than the top. If putting the thing in a box (to reduce the heat out the side walls) isn't feasible, turn the flame up make sure your top and bottom vents are wide open instead. You're using more fuel then, but it's going toward the top of the smoker; and the fraction lost out the side walls is then less.