Never mind, I found all 8 of them here:
http://eab.abime.net/showthread.php?t=58121
The glitch was introduced in 2.3.2 beta 4. All betas after that have the glitch, 2.3.2 beta 3 and earlier work fine.
I'm wondering if it's this modification in beta 4 which caused the issue:
"Stop the cpu and wait until blitter has finished if any blitter register is accessed while blitter is busy and cpu mode is fastest possible".
As stated, setting immediate blitter does not fix the glitch, so this appears to also affect immediate blitter.
(I know AMOS 3D makes heavy use of both the CPU and blitter, it requires fastest possible CPU + JIT + immediate blitter + disabled Vsync for best performance.)
If it is this which causes issues, could it possibly be moved to config options?
(Perhaps a "CPU wait for blitter" checkbox, on by default?)