And Peter, did you try out the suggestions that were made at that time?
Can you be a bit more specific? I remember only one applicable suggestion, which was to set a system variable before leaving the ISR. Didn't work, at least not under QDOS.
Could the effects Peter mentions have anything to do with the cache?
Same with caches off. The effect only happens in realtime and is hard to debug, it may have a completely different cause.