I have not programmed any of the my Model F's in awhile, but I believe you will need to provide a different key that will allow to you go back to the base layer.
First of all, you are aware of the differences between the Fn keys and the Select keys, correct? Any chance that you could take a screenshot of your layer conditions page? For now, perhaps you could add the "Select Base" key code to layer1, so you can return to your Base layer when the keyboard is stuck on layer1 (if you haven't tried that already).
I've had the issue with phantom keys, and I'm thinking that might be a bad controller or bad PCB, because nothing I do seems to solve issue. Perhaps it would be a good idea to add extra shielding or grounding to the controller and see what happens. Also, make sure that all your dead keys were identified when you were finding the correct voltage threshold. You need to find all the dead keys BEFORE using auto calibrate.