It looks like you have a lot going on...for now, disable all your automations linked to the thermostat except Thermostat Controller and Thermostat Scheduler. To do this, check the box on the left column on the Apps page to disable the other automations, like below:
If you don't see those boxes, click on the grey "X" in the header of the apps screen to enable them:
For that use-case Thermostat Controller would be the recommended approach, since it takes over the thermostat's settings, and changes on the thermostat will be overridden by the settings in the Controller/Scheduler combo. That may be what's happening to you now, if you have Thermostat Controller engaged while trying to use other methods/automations.
