Thanks for all your help. Haven't been able to find any specifics in log files etc, but I did notice that when returning to the flight from the escape menu, the windows were showing the flight seat texture, rather than the sky! In addition, the red text I always show (CTRL+Z) was corrupt.
I disabled 3D cockpit and went for low res 2D instead and for now, this looks to have fixed things. I also unticked AddOn scenery in the settings menu, will add that back and see what happens.