I finally got this finished! It was a difficult one as I was only getting the odd 20mins at a time to work on it. I had a faulty replacement 6821 with no scclock output to the alpha... I initially swapped this but swapped it back when there was no improvement, but found it later when I came back to check it with the scope... I ending chucking this mofo 6821 across the room.
The original alpha had a dead FET but no hole in it like usual. Which is 95% the tell tale sign...on the 12v ones anyway... My spare alpha had an issue where it wasn't internally Resetting... even though the reset from the 6821 was good. On the first boot with it, it always stopped the whole machine dead from coming out of reset... nightmare!
I sussed out what this was by unplugging each plug on the board to see what area the fault was. With the alpha display unplugged it booted perfectly every time. The second boot with a new 6821 and the reset fault display worked flawlessly- any other resets or door closes after that and it was just garbage on the alpha display. 3 separate issues all in the same area! I recapped and changed the FET on the original alpha and presto it finally works... resets nicely and displays perfectly every time.