Sounds to me as if the fusible is sticking to the needle, which will certainly throw off tension erratically on stitches. Fusing melds the fusible with fibers. My bet is that your light fusing left a lot of the fusible unmelted. The needle is sticking to the fusible, and the thwack-thwack is from the fabric top and backing sort of peeling the fusible off the needle as it goes up and down.
What kind of marking did you use? I would experiment with fabric scraps to see if you can use higher heat on the markings and still be able to remove them later. Other than using higher heat to actually melt the fusible in the quilt batting, my only thought is to change the batting. Better to unpick everything now and change the batting than try to deal with this problem throughout the quilt (assuming you are unable to use more heat).