A while ago I had an Amiga 4000 that boots fine with an A3630, but A3640 (or A3660) won’t boot.
I spended many hours to find the problem, couldn’t find it. So I left the board for a week or two, after that I inspected everything again, and everything seemed ok.
There was one thing I didn’t changed/tested, because it seemed good.. The 28MHz oscillator on the mainboard.. Changed it with another one.. booted the system with the A3640 board again.. And and and.. IT WORKED!! YEAH!! The signals on the scope looked equal.. but apparently there was a minor difference..
So the 28MHz oscillator can fool you!!
I forgot to make a blog post about this, but John Hertell faced a same situation.. I pointed him to the 28MHz, and yes that was (again) the solution.
I talked about this with John, he told me he had seen this this with the 50MHz oscillator on some A3660 boards that didn’t boot.