Perhaps I should clarify it doesn't seem to be ALL workshop files, it just seems (?) to be selective content which triggers it. I've still got quite a few others items/missions installed but the screen/map flashing now seems to have stopped.
I didn't uninstall everything, but systematically worked backwards from my most recent installed workshop files (as the problem was a recent one for me) until the flashing bug stopped.
Good hunting Bohemia!