Flexi contour cut problem

[yamaha581]

I have been using illstrator and setting up contour lines then I would take them into flexi and set them up with the contour cut and the reg marks so that I can cut them out in flexi. Now for some reason when I open the files in flexi all of my cut lines show up but once I select them all and go to contour cut to change them to the gray only the outside lines show. If there are any cut lines inside of the main graphic they do not show up. If I select the whole print the lines all show up but when I go to contour cut it shows that it will not cut out the areas inside of the main template. I am using this for motocross graphics so it is only selecting the main template not any of the cutouts for the bolt holes if that helps.

 

[signcrafters london]

I always apply my contour cuts with DesignCentral and make sure the "with holes" box is checked for that very reason. It also makes it much easier to change other variables such as offset, too.