Well, to start, it’s not just ATC, all the electronic gages in the cockpit are flashing at the same frequency as the ATC display as well.
I’ve not heard of this one before.
It could be a conflict with a mod of some kind.
Mod conflicts can cause issues with electrical systems, but normally the electrical system just shuts down completely when that happens.
You may want to try the sim in safe mode to eliminate a mod as a cause.
Although you wouldn’t think it could be port related, as it works with others, you may want to try another port on your PC for the controller, just to see.