I have noticed why its not working, but im not sure its something thats suposed.

Now heres the issue:

 

I have the SW:TOR mouse form razor, and thereby I have added a lot of the quickslots buttons to the mouse side buttons.

 

Now I want to control the AoE skills and passive skills of my companion, so I bound them to the Alt 1 and 2

 

this works everytime the companion has this bar equipped. (showing)

But when its its not visible the short cut dont work..

 

Now, what am I doing wrong? and is there a way to acess my quick slot buttons as a shortcut when the bar is not fully visible ?

You're not doing anything wrong. As far as I've been able to figure out, shortcuts to action bar abilities simply don't work if the action bar is hidden. This applies to both the companion action bar and your own.