Did you get the problem resolved with your Accuquilt? I haven't had that problem yet so not sure what happened.
Couldn't tell exactly by your post but did you have 6 layers doubled for 12 total layers? OR 3 layers doubled for 6 total?
Generally, they will cut 6 total layers. If fused with fusible though only cut 4 layers of fabric through the cutter.
Good luck!