I'm good now AC/DC HACKER, and figured out what caused the issues
My issues were as detailed in my edit i.e. having 3 x disk drives and 800% Floppy Drive Emulation set (which works fine in v4.4.0).
So now my config has been adjusted to be:
- CPU = 68020
- Chipset = AGA and Cycle-exact (Full) ticked
- ROM = KS ROM v3.1 (A1200)
- RAM = 2MB Chip & 4MB Fast
- Only 2 disk drives enabled and no more than 400% Floppy Drive Emulation.