Not a bother at all!
Uhm, you don't really have to hit the brakes. I do at first, let them off and roll to an area I please. Try touching back down to continue capturing it -- it should work with just one plane.
However, the counter will not move if there is an enemy aboard the ship as well. This sounds like your problem, because when you and a team mate land as you said -- it begins to capture.
Also for a quick getaway: Once you've deployed your landing brake, keep it on and crank your engine at just under half speed. That way you just remove your brakes and you'll be off!