Remember that you're playing on an emulator and will likely be using the controller to like, move and stuff. So move that controller anyway. And, like magic, it actually goes away with a mere flinch. If you're too lazy to even do that, a mere "nag screen" is the least of your problems.
Or, get and play on the actual hardware/game/PCB/arcade cabinet to avoid this.
No. The real problem isn't with the screen, but your failure to accept the screen. Work on You.