this is just a shot in the dark,but i had a similar issue long ago on a 4000 that someone had stuck A1200 roms in for some unknown reason,it will boot with 1200 roms but you will get trouble like you describe. if memory serves the chip ram showed up fine but fast always had a problem.Just something to check.
i would suspect the simms you are using off hand otherwise.Can you try it with 2-8MB simms instead of the 4-4MB simms?
dirty/tarnished simm slots could do this,but i would suspect you would be getting odd size ram reports.
Has the board you are working on been battery damaged in any way?
mech