I have started having a similar heater issue, a random period that may last an hour or less or more,with one side being cold, the other side hot. I think I will replace the air temp sensor on the driver side, it is cheap and may be starting to fail. The actuators seem to function, since sometimes the air is hot , sometimes cold,depending on its mood.
The control module unfortunately may be starting to fail, which is over $100. Maybe a bad solder joint, a capacitor going bad, a microprocessor starting to fail. The temp sensors are many, so I will remove to get the part number.