Hi,
I had problems on my board that may be from the same misconfiguration. In my case, all was well until I did a movem.l instruction, popping many registers off the stack.
The punchline was that I had configured the RAM for CAS2 and the CPU for CAS3 (or something like that); essentially because the table headers describing the SDRAM controller were confusing.
So... all worked well until the CPU and RAM got a chance to burst some data, then it screwed all up. Sounds similar to what you're describing.
Good luck!