You can check the number of colors in a PDF file using the PDF Pre-flighting feature in Adobe PDF Professional by following these simple steps:
The instruction below pertain for Adobe V9. (If using other Adobe PDF Professional then look for the Output Preview window)
Choose Advanced>Print Production>Output Preview to launch the Output Preview dialog. It will look as shown below:
Click on the Separations Choice in the Preview window. You will see the number of colors in this particular document when it was created. Here you’ll see there are process colors (CMYK) and a spot color, Pantone Violet U. Here the U designation indicates the UnCoated version of the spot color assigned form the Pantone list of solid spot colors. The inclusion of this spot color requires either that this spot color be separated and printed as a separate color or converted to CMYK for printing along with the other process colors.
By checking and un-checking the separations you can visually see what elements in your document contain that color.
If you are submitting a file which is supposed to be printed in 1 Pantone Color, then there should be just 1 Color showing up in the Separations Box. For a 2 Color Print Job there should be 2 Pantone Colors, and so on.