I think that they DO NOT have the ability to fix this problem or they just DO NOT want to.
Just like EA style.
Okey, here is the solution from me, its work for me.
The problem still there, so you need to do this solution everytime when you do those flashpoint.
First, you must know when the Bugged hyperspace jump will start.
(In Esseles, the jump is right after the conversation)
1. make the game screen to "FULL SCREEN" mode.
2.1 Do the trigger button and make the hyperspace jump start.
2.2 You need to HIT "ALT" and "TAB" at the same time on you keyboard to make your screen back to desktop.
The point 2.1 and 2.2 need to be complete in about 1-2 second, and better at the same time.
3. Relex and wait about 10 second, and than HIT "ALT" and "TAB" back to the game.
4. Now, your ship finally pass the Esseles Bug Field/ Black Talon Bugfield, and enjoy the rest of the game.