Still sounds like you might have picked up a faulty HVAC controller, but maybe not.. Try this for me: on the far right of the back of the controller, there's a gray connector. The green wire three from the top, see if you can remove it from the connector, OR, the green wire on the switch connector (which should be in position "D"). This is the A/C Disable wire. If that does not fix the mode door and A/C problem, I would sincerely look into finding another HVAC controller.
Also just want to verify something, when you redid your connector, you put the orange wire next to the brown wire toward the outside of the connector right?
For that matter, try using the A/C switch with the fan switch connector unplugged completely. That should rule out the A/C Disable wire directly.