While looking at temperature averages at the end stations just before noon, I noticed that the B Temperature sensor at each end station was reading ~1 degree F higher than the other 3 sensors. I took the B sensor out of the equation to try and help stabilize the temperature. 

I made one other change and that was to switch the supply air temp control from manual to auto reset.

During this upgrade to the entire HVAC controls system, many of the older programs were copied and because of the nature of the older system, many of the points were set to manual. We have been working diligently at trying to catch all of these settings but inevitably some have slipped through. We continue looking.