@Amicol : "Will buying a Fast IDE get rid of these issues. I haven't taken the plunge yet as I've read it can't be installed together with the Indi AGA 1200"
-> Getting a FastATA will not help you get rid of these issues as I have two (MKI and IV) and it changes nothing at all. I personnaly think it comes from the overall IDE CPU relative process (will test asap with an SCSI disk.
BTW I use both FastATA with an MK2 without problem, but you'll need some ROM socket adjustement in height.