The SCSI on my A3000D is very fussy even with the -08 WD chip. It seems to be the fastest and most reliable with just 1 internal drive.
My only thought would be to double check that your termination is set up correctly. The drive on the internal connector should be terminated, as well as the last drive in the chain on the external connector.
If the extra drive(s) are installed on the cable inside of the machine, then remove the termination from all of the drives but the last one in the chain.
