P28 Not Finding Registration Marks at all

[PlaneMaker 0]

My prints are good, I’ve tried different sizes and widths and offset of the marks, but the P28 just moves to the text (usually) and then it starts beeping. 
Questions:  

does it matter where the vinyl is placed on the cutting mat?  It shouldn’t as long as the carriage is set over the first registration mark. 
 

also, I have to print on 8.5 x 11, but I have the mat in the software set to 12x12 by default, because that’s what I normally cut. 
i am cutting two 5x5 square decals with a 3” hole in the center.  How do I tell it to cut the center, too?  I am telling it to only cut the color of the layer that just has the outline that I need, so it may all work if it would only recognize the registration marks.  Marks are black, vinyl is glossy white under marks, but decals are blue.  

 

[Wildgoose 4,200]

What software do you use with the P28 to interact?