I also experienced this reversal, but I'm not sure if I'm imagining this, but it wasn't reversed all of the time.
(This was also fatal when playing the ship with self-destruct I would suggest that you should have to press the button 2 or 3 times to self destruct, as the Shofixti ship used to be, with the state of the self-destruct switch being shown at all times.)
-> I would also add that it's frustrating to have to use the mouse while in menus, and picking my fleet. The controller should be fully supported so that the whole game can be played with controller only, if desired.
-> The mouse pointer does not auto-hide and gets in the way while a battle is on.
Here is an interesting review of the Beta, with which I mostly agree: destructoid article