Also, sometimes with eq when you do the alt + enter, it will change your UI scale obviously. But, when you try to change it back, sometimes at least for me when I accidentally hit the command (which I changed), it doesn't scale back at all. Even reloading the ui doesn't help, so I have to set things back up.
This was a major problem when I was using isboxer also.
I would stick to windowed mode, makes life much easier. Also, setup mq2hud for managing the team, that way you don't need to swap around.