Would you be willing to send me the file so I can look at it? It's probably some little thing that can be hard to convey without looking at the file.
If the mat size is different, then you want to be sure that the rectangles will be on the cutting surface in relation to your paper. I think I know what the problem may be. When doing a print and cut, because you have to line up the registration marks, your origin is usually off the paper so you have room to line up the registration marks - right? So the origin won't be in the right place respectively to cut the rectangles. Off the top of my head, I think I would make the mat and the paper the same size and when you need to cut the rectangles, reset your origin at the lower right hand corner as close to the point as possible, and then cut the rectangle layer in WYSIWYG. I think that may work - you just have to set a different origin because of the print and cut.
If you want to email the file to me I will give it a try.
admin@silverbulletcutters.comI hope when I see it that will crystallize what I am thinking in my head - or change it altogether!