MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
They are indeed designed to go right to the limits of the Simple metal's build area. I can't speak to Cura, because I used Slic3r to do my slicing, however I found that if you have it printing a Skirt or a Brim it may be pushing those outside of the printable area. you could try printing them with no skirt or brim , or on a raft possibly. I'll also upload my GCode for the middle pieces ( no heated bed was accounted for in them though )
as for issues with the button circles, I'd need to know more about your setup , what are you printing onto? do you have a heated bed? hope I've been of some help! look for MT.gcode and MB.gcode in the files section if you want to load them up in Repetier or something.