I would recommend getting a tech to check it out. Believe it or not, it is pretty easy to get ducts crossed when you have been working in an attic for a few hours and sweat is dripping in your eyes; they all start looking the same.

Bottom line, the thermostat should be located to sample and control the zone it controls, anything short of that and the installer did not do it right.
I can't see the system in question, but it sounds a little screwy to me.

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Jim Luttrall
Mr. Inspector.net, Inc.
Allen, Texas 75002