I have figured it out. It is Tobii Eye Tracker!
If I close the tobii experience app it works every time showing Frame Gen Lag and the green tick.
If I maximize my game, confirm seeing AFMF is working with Frame Gen lag, then restart tobii experience, frame gen lag disappears and AFMF is disabled.
Oddly when I close tobii experience and tab back to my game it maximizes differently, as if with tobii enabled it’s not properly full screen.
Does anyone else with issues use Tobii Eye Tracker?
Bug reported here AMD Fluid Motion Frames stops working with Tobii Experience app open