Whee this was fun, involving oscilloscopes, digital timing, seriously staring at code, lots of AVR flashing and 2x mile-long thinkin' walks. Can you do an AVR update from the "online repository" and get the hex file from today? I think I got it ironed out, and I can even trigger lid mode and turn it back off in under one PID loop (1 second) which was almost impossible before due to all the timing overlaps. I can get it to not detect a button press sometimes if I release the button as fast as I can as soon as it clicks, but watching the oscilloscope waveform the analog line isn't at 0 for about 35ms but really has only stabilized for about 10ms so there's almost no way to detect that without adding more circuitry or not sampling the probes as much.
Something to note is that if you are on the No Probe home screen, there won't be a lid mode indicator LED light up for up to a second (because the LEDs update only once per second, where the LCD text would update immediately but you can't see it because it says No Pit Probe).
HeaterMeter 20160415B is the version number