sethatl I have the Smoky Mountain Series 3600 Smokers in both charcoal and gas versions. I can say from experience that I've never had any temperature variance in a chunk of meat that drastic. Even when doing multiple briskets or butts I've not had that much difference between meats on separate shelves (even without rotating). The GOSMS smokers are pretty evenly heated and recover temperatures rapidly after being opened. I can't see any reason for the one half to be finished and the other not. I'm at a loss
How much have you used this smoker? I've had mine for 8 months and have used it dozens of times. Have you done other cooks that didn't have this temperature difference? What types of meat? BBCue-Z, GBitto, and my brother-in-law also have this smoker. Yahoo has a discussion group for owners of the GOSMS at: http://groups.yahoo.com/group/smokeymountain/
Hope you find the answer, let us know when you do.