It might help if you put them in so the fat part of the butt is opposite the fat part of the shaft, if you don't do that already. I put mine in my rugged so the cue tip is facing up and the butt cap is facing up. But I only fill 6 of the spots in my 3x4.
I believe one of the selling points of the JB cases is that you can tip your case upside down and none of the shafts/butts will come spilling out - the idea being if you accidentally knock over your case (or someone else does) when it's opened, your cues won't go flying across the room and get damaged. Mine also was quite tight in the beginning, but after a bit of use, the fabric in mine compressed some so it is not so difficult to remove from the case anymore.