JAV I belive what I am going to say has been hinted at but not talked about in depth. I also believe the calcs that were originaly run were most likely correct except for the fact they should have run the heat loads, upper and lower, seperatly and not together. What this would have done is to give the downstairs part of the house no ceiling heat load and therefore lower cooling requirment downstairs. That would have required a different alocation of cooling than you have now which is 2 1/2 tons upstairs and 2 1/2 tons downstairs making the upstairs unit carry some of the downstairs load. This is often the problem with two story houses especially when there are rooms downstairs that have high ceilings that go into the upstairs space as you said you have. I won't go into if or not your systems are running properly. You said that this has been a problem from the begining so it all boils down to this: if your mechanical units were running properly on start up and continued to do so into your first cooling season the problem lies in the fact that your system designers never condidered the fact (or did not want to address it) that your cooling requirement up and downstairs were different (and they are) and how they would deal with this difference and still maintain comfortable air flows. The reason I say comfortable air flows is because to increase cooling they would have had to increase air flow (or volume or cfm). What needs to be done without having to change unit sizes is to give some of the upstairs heat load to the downstairs unit. One way to do this is to connect another return air duct to the downstairs air handler and install the other end of this duct or the pickup end as high as possible in the upstairs space such as the upstairs hall ceiling or a high wall. The location must be open to the major portion of the house. Not in an area that is closed off such as in a bedroom. This duct should be large, sizing is very important, also the farther it has to go the larger in diameter it has to be. If you did somthing like this you would have to keep the fan setting for the downstairs unit to the on position all the time during the cooling season to be very effective, also at the connection of the new additional return air on the downstairs unit you should install a damper so that you could partially,not compleatly, block off the existing old return during cooling and force the air handler to pull from the new return, during the heating season so as not to disturb the air movement during winter because winter heating is good the way it is move the damper so as to close the new return. An important thing about a damper set up to do this is that you never want the damper set up in such a way that if it loosens from its setting that it would starve the air handler of return air. Installing a return like this esentially destratifies the house so to speak. I hope I have made myself clear and helpful. Regards bd