If you are FM quilting, I'm assuming you're using a FM or hopping foot, and have your feed dogs down or disengaged. In that case, the machine should not be feeding the fabric at all, it is the motion of your hands that moves the fabric. So what might be happening is the FM foot is not hopping high enough to clear the extra-thick seam.
Some machines have the ability to adjust the amount of pressure on the pressure foot. If yours does, you can lessen that pressure so there is more 'give' when pushing that thick seam underneath.
If not, you may have to avoid the seams, or, and this will sound funny, take the quilt sandwich and hammer those seam intersections flat. There was actually a vendor at a quilt show once selling rubber mallets for hammering down seam allowances!