Right, so even if I select the 68000 profile and save it the ACA1232 is still active then! Didn't realise this as the ACA500 manual isn't very specific and the ACA1232 manual doesn't mention the disable jumper! I can wire a simple SPST switch up the pins via a 2 pin connector.
Still doesn't explain why the profile I save is getting lost. I save it and it works then somehow it gets reset?