Just a note to say I fixed this issue now..
This is what fixed it in case anyone else has issues.
1. Lock the car with the working keyfob, keep it away from the car, in the house or something, keep it well away
2. Ensure you are using a new battery with the second non-working keyfob, make sure the LED is flashing on the fob (I used cheap batteries I had, and the LED was very faint, changed them to more expensive batteries and thew LED glows much brighter.. worth spending a little more, don't get JCB batties from B&M store
3. Open the car door with the manual key inside the fob, turn the key to open the door.
4. Immediately place the dub keyfob in the centre console area where you charge your phone, where the key symbol is.
5.
This is the step I was missing.... push and hold the clutch (for manual cars) or break (for auto cars)
6. Press the start button, a message on the dash is shown
Remote Control Key: hold ket against the designated area
7. Press the start button again with the clutch held down.
The engine starts and the key fob is now re-synced and can be used to lock and unlock the car.
Notes: I had to perform steps 5, 6 and 7 twice before the fob started working fully.