Lots of variables we’d need to track down: the particular SCSI controller, chip revisions, driver versions, which CPU card (the dreaded rev 3.0 3640?), FFS version, other expansions, mask and max transfer values in the RDB, hacks running in user-startup or WBStartup, etc.
Personally, I’m betting on it being a wonky Expansion Systems DataFlyer controller. Had one of those in my 1200–nothing but unexplainable trouble!