A couple more thoughts. It sounds like you’re using the controller to keep the fridge at our near the temperature the fridge wants to be at anyway. (If so, I’m not sure why you need a controller, but I’ll just accept that and move on.)
What you probably have then, is the two controllers fighting each other. When you use an external controller, the internal controller does not go away. if you want to use the external controller for tighter control; set the fridge to max cold, figure out how cold that gets, then set the external controller to something higher. I’m not sure how much higher you need to go though.
Finally, verify those factory settings. The default “Compressor Protection Delay Time” is only 2 minutes, meaning it should stay in protection mode for no more than 2 minutes. From your original post it sounded like it was staying in protection mode for much longer. If the setting is ACTUALLY 2 minutes, and it’s not coming out of protection mode, you may need to call support to find out why not. It could also be that hysteresis is set lower than the factory 2 degrees. If your fridge rises 2 degrees in less than 2 minutes, you should invest in a better insulated fridge.