I have tried reseating the large flat cable with power on, this seems to reset the entire system as if I have cycled the power cable.
I have also run the self-test (delay and boost held down while powering up) and I could go all the way through, no issue with any buttons, LEDs or encoders. The unit still freezes when powered up.
The ATMega would be nice fix, surely it is programmed though? I can attempt to desolder and dump it but I imagine it's code protected.
Would a dump of the main socketed ROM chip help you out with your unit? Mine has a v1.2 sticker.