I can't see why I would have to do it but is it better to do a fresh OS3.9 installation??
Yes, it would. At least you don't loose anything by trying.
Maybe try to set the SCSI settings to auto all the way through in the SCSI menu, and setting the speed of the ram to 70 ns.
You could also reflash the card with the latest flash. This sets all settings to default. If it works, then you can tweak the settings afterwards.