Hi,
Are the drives jumpered as Master and Slave accordingly or are either set to Cable Select? This might sound odd, but if you have an extra 40 pin IDE cable, try slicing the pin one (usually the red wire) between the motherboard connector and the first drive connector. This helps the Amiga see some drives - I have had to do this on some A1200s and A4000s depending on which model of HDD was installed. Try the jumpers in different settings CS vs MS. If you have an extra IDE cable around it might just be worth a try.
Good luck!
-G
