I know this thread is ancient, but I have exactly the same issue (different OS though).
Supra WordSync, OS 3.2, won't format in WB (gets to the end and says 'Not a DOS disk'), even though it partitions etc. correctly in HDToolBox. As soon as I restart the machine, the partitions disappear (basically looks like the RDB isn't saving). This happens with both of the SCSI drives I've tried, so I'm suspecting it's the card now, even though it was working when it came with the A2000.
@utri007 Did you ever manage to fix the issue?
I don't really use the card, but I'm looking to sell it on eBay, so it would be nice if it was working!
Cheers,
Gaz.