When you create the art or look at the customer art, in the search pallet, double click on the color to confirm that it is indeed a spot color (Pantone) or a custom spot color you created. It sounds like your colors could be assigned as a process color instead of a custom or Pantone color.
If it is indeed a spot or Pantone color, then maybe your art elements are not 100% solid.
If they are, then the issue may be a rip glitch of some sort.