***SOLVED*** I have finally managed to fix this for myself by running through the following:
Load up to the main menu, Options, Assistance, change the preset to “All assists” - this is the mistake I was making, I individually changed each setting to on. DONT DO THAT, change the preset at the top of the page!
Apply and save the changes. Close the sim. Restart the PC.
Load up to the main menu again, Options, Assistance, now change the preset to “True to life” - again making sure you do it via the main preset. Apply and save, close the sim, restart the the pc again.
Then you should be good to go! Load the sim up, start a flight, and the ATC box should pop up!
Hope this helps anyone else having the problem.