This is going to sound dumb, but have you verified that Caps Lock is off?
I assume you have re-booted and ruled out those kinds of things? What about pop up windows in Non A2A aircraft?
Obviously if you screwed up the aircraft config file when you added in the skins, then that could definitely cause this to happen. Go back to your original config file and if it works, then you will know. It's probably an extraneous comment delimiter. If so, then add in your repaint blocks more carefully next time.