Are you saying that your house is getting too hot or that a 2 stage is only heating on the second stage?
If its the former..the 1st thing to look for is a short between the thermostat lines somewhere between the mother board and the thermostat on the wall. (worn insulation between both lines or over metal, maretts that are missing on a spliced connection, a nail or staple through both of them, etc.)
I hooked up the thermostat to the furnace with a short wire. Same result - once it starts a heat cycle it won't stop. Turning the thermostat down below room temperature doesn't stop it. Setting the heat-off-cool switch to off doesn't stop it. Anyone have a troubleshooting manual?