For anyone interested this is now resolved.
Worthy of note if anyone else suffers this;
Removing the small ‘back up’ battery ONLY looses the time and date data. It does not instigate a full reset procedure. Everything else stays the same.
If there’s a full reset from scratch option on the 1DsII Canon are keeping it to themselves, (other than the restore default menu options mentioned in the manual).
The camera whose settings got loaded onto my camera was running the same firmware version, but was used with Lexar cards as opposed to my Sandisk cards. It seems the other camera has had problems with card writing in the past, which may or not be connected to this.
After calling Canon’s UK service agents Fixation, a very helpful team, the card writing was returned to normal after using ‘clear all custom functions’ and ‘clear all personal functions’ menu options.
Curious given that there is nothing in those settings that controls card writing and I’d reloaded the firmware and reloaded my own custom settings too. I guess these settings may do a lot more than just clear a few menu items based on my experience.
I still haven’t got the bottom of why the EXIF data is still showing the incorrect number in the shutter count, but I’m still researching that one.
Thanks everyone for your help.
Paul