You could reflash your card with 1.187 firmware to finish your 5 cutouts. I assume that the problem is in the newer firmware. I am thinking that a bug could have been introduced when the "flip jig" feature was added.
I will try some experiments. It would really help if someone had a simple mpc which recreated the problem. I take it from you both (Perry and Dick) that the problem should arise for a 3/4" thick double sided project on a 1/4" thick sled. Carving on the back and cutout on the front.