Some new theories: system appears to be stable in 8bit screenmodes; 16bit or higher cause it to crash. I'm using a CVision3D. It looks like P96 was updated as part of Update 5 - perhaps a bug was introduced? ReAction is still the most common trigger, although I've had windows from some other programs (DOpus, MUI) also cause crashes. Never Workbench windows, though.
Sometimes I get a Guru screen (the traditional Software Failure red box, not the Grim Reaper) with error 80000002.
It might be worth trying just AGA/ECS screenmodes without the CV3D connected.