ARMA3 stores user's profile in home directory. You can delete it and Arma will create a new one. Or you can add -profile switch to Arma launch options to create one with a different name (by default it's name of your account). I did it to make sure that starting with a new profile fixes the problem and that it's not caused by bad configuration.

On the happier note: I manually edited config files (somehow) and launched A3 in a window (added -window to launch options). But now it sometimes hangs on before the intro is played and only the black screen is displayed. I think my hybrid graphics (integrated Intel + discrete nVidia) is to blame.

I tried with clean account and all mods removed. Same problem.