If I make a brand new Layout, and apply a NAMED page setup to it the paperspace origin is 0,0 Inked area limits..
I suspect this has to do with you cutePDF paper sizes...not having that pdf writer installed I can not test to verify this hypothesis.
Cad Manager TIP:
You will want to do a much better job of Naming the Page Setup; try something like Page Size_CTB_Plotter Name.
Example: 36x24_Color_CutePDF
In this manner once you have all of the various printers, plotters, page sizes defined within your template (yes ALL of them in one template) it will make it much easier for the users to select the proper Named Page Setup for their output needs.