I assume yours is an Amiga 1200 with Blizzard 030/50. I've had problems with Quake running on a similar system to yours due to overheating of the FPU. Now the game would work ok for about half an hour and then start to give weird graphic corruptions in the game and finally guru the machine to a halt. I used a 40 mhz clocked FPU instead of the recommended 50 mhz. Cooling both the CPU and FPU could help in your case. Problem is that the 1200's cramped case doesn't allow for extra fans or cooling bodies. Towering the system would certainly provide ample cooling. Otherwise, you could at least try running the amiga without the trapdoor lid on and maybe rising the entire case on some filt furniture stands or something. Good luck.
