Malgor,

One last thing... make sure that when you start up your game, you press "Home" to activate SLOT 1 key maps. And if you click into your alt's window to focus and activate it, you need to press "Page Up" to activate SLOT 2 key maps.

Anytime you are playing from your main, just start out by pressing "Home" a couple of times and if you switch to your Alt, just press "Page Up" a couple of times. I have a feeling that will solve your problem... hopefully.