Spot colors from placed graphics don't show up in the color pallette. Running Quark 6 on OSX.3.4. The color pallette only shows, for example, PANTONE 186 C. In Illustrator the same color is called out as PANTONE 186 CV. The CV version doesn't show up in the color pallette.
When you print or export a PDF the extra color plates show up. You need to be able to first see all the colors associated with the file. Then you need to be able to marry the colors up for output. For example when going to press PANTONE 186 C, PANTONE 186 CV, *PANTONE 186, 186 RED and PANTONE 186 CVU probably all need to go onto the same separation.