You would think in the 24th Century that pop up screens wouldn't stall a ship, but in Cryptic's Universe it does. Ad it does it with perdictability. Btran for instance enter Enemy Confrontation and first thing you see is pop up. No degree of unperdictabilty of entering a uncharted region of space. Shouldn't that happen after you have sensor scanned the area and assessed the situtation?
But it doesn't stop there. Just as you distroy an enemp ship a popup happens again so quickly that you can't even pop evasive to get away becasue it forces your speed to zero. Point here is that pop ups like that shouldn't be be causing your ship's speed to zero. The other ship didn't hit your engines and they are not in need of repair. So why are you stopping. Sucide Wish? Or is it for the Dev's amusment to try to get your ship caught in the blast.
I know for a fact that this space combat is based alot on StarFleet Command III. I used to play it and also played in beta here. No where in that game does a popup happen and force your speed to zero. And I know for a fact that in all the star trek series I have never watched that a popup affects a ship. My point here is that the dev's need to change the point of where those happen.
Those pop ups keep the game from feeling fluid, just as battle is supposed to be, It is in PvP, so why not PvE. I am not saying remove them....just change the timing on them. IMO.
You can't adjust when the pop ups happen unfortunately but you can make it so you don't stop moving. While in space go to options under controls and select "Keep moving during combat dialogs". I also move my popup window to the upper left of my screen to make things easier to see when they do pop up.