OK Solved it myself, feeling pretty dumb about it too!
Anyway, for anyone else benefit, here is how it's done.
Take the Apple Remote for you other machine (in my case the mac mini) and pair it with that machine
- This will ensure the ATV does not respond to it
Learn the ATV to your 3rd party remote
Now here is the trick I couldnt work out:
Take the Apple Remote for your ATV and pair it with the ATV and THEN JUST PUT IT IN A DRAWER SOMEWHERE.
The pairing on the ATv stops it from responding to the Apple Remote from the other machine, so you are free to use your 3rd party remote for the ATV and your other machines Apple remote for it.
Hope this helps someone!