Ok Guys, just got back from working away. Thanks very much for all your help so far.
I read all of your comments, and can now get the machine to boot from the CF HDD even when the ACA1221 is fitted. Once at the desktop I see all my drives and files. Games/files run perfectly. It is still not right though, as I cannot get it to work 'automatically'. I will try to explain. Please see the images they may help you understand what I don't LOL.
http://www.dropshots.com/RSwipeCA/date/2016-12-09If I switch on the Amiga whilst holding both mouse keys I can go to the boot options screen (please see the image). If I select DH0 it will boot to the desktop. If I reset I have to go back and reselect it again, I am guessing it doesn't remember the previous setting. Also, sometimes by holding the mouse buttons on startup it will got to a different screen ( the picture with 'Max-Mem Sequence' options listed). Out of those options if I select 'Reboot' it will boot straight into desktop and everything is perfect.
If I select 'Boot with no startup sequence' I get the Amiga DOS prompt screen as shown. It doesn't go to the 'Tick' screen.
Also, there was mention of adding a '-p' to slow the system down in order for it to have time to boot from the right drive. How/where to I go to add that '-p'?
I will admit I'm a bit lost here, I assumed adding the accelerator would have no effect on the booting of the system. If I have to hold the mouse buttons down each time I boot in order to select 'Reboot' from the Max-Mem box to get to desktop, then so be it. But I am guessing that shouldn't have to be the case.
I hope this, plus the images makes sense to you guys.
Thanks again.