sounds like it could possibly be a couple different problems from oversized system, defective stat, breeze at stat location, stat being heated up by other means, air leaks......etc.
You questioned the load calc earlier in another thread. And it has been suggested that the installers have re-arranged some figures to put them in the clear.....
My opinion and advice would be to seek a professional opinion and diagnosis from another reputable contractor in your area. You will more than likely have to pay for their time but you may get the much valuable information you need.
If you've already had issues with this system and installer, I would also recommend you purchase the extended warranty for 10 yr parts and labor from the contrator. That is assuming that your going to keep your current system and contractor. I hate to see you get past your current labor warranty and start getting hammered with high repair bills.
We have offered as much help as we can without looking at the system. You are going to have to either trust your contractor or find another one to come give you a second opinion or other options.
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If you don't know, then don't do. If you don't know and still do, then be prepared to pay someone else a lot to undo what you did and then do it right.
If you do know, then do. But do it right. Otherwise, you may not be doing it long.