Navy Flag Ship battle

[ASuperStitch]

I am hoping this has happened to someone else and you can help me here.

I can not board Navy Flag Ships. I engage them we battle the timer bar comes up that says ready to be boarded, other ships gather round and shoot grapples and I see there lines catch onto the Navy ship but no matter what I do or how I do it I never get the option to fire the grapples at the little green circles and therefore am never able to board.

I watch helplessly as the Navy Ship I disabled is boarded by others and battled and sunk and I get no plunder, no rep and worse no credit for sinking a Navy ship that I need (or have needed) to complete a quest.

What am I doing wrong or not doing at all?

How do you get the circles and then the option to use the grapples and eventually board and fight and sink the Flag Ships?

Thanks if you can help.