Okay so I might have figured out something important.

Previously I had a Turbo Timer fitted and when this started playing up I thought it was the Turbo Timer so I had the Turbo Timer removed but I am not entirely sure whether I've removed it entirely as I didn't fit them to begin with but what I did was simply trace back the black box and remove all that and reconnect the normal plugs again that was branched to the Turbo Timer so I thought all that was removed completely.

But now I just checked the timing with the check engine light on after switching off and sure enough after 60 seconds the check engine light turned off and I heard that click noise once just like it used to when I had the Turbo Timer and it was exactly set to 60 seconds before.

So now I've isolated the problem but just can't figure out what's causing this to still operate... could it be the ECU is learning this previously and still thinking the Turbo Timer is still on? Should I reset the ecu? But would resetting the ecu change and delete all the tune I have in there?