I have two separate InDesign CS5-documents that have the same Illustrator CS5 .ai-file placed in them. One of the documents honors the PMS color but the other one turns it to process color. I´ve heard there might be trouble with .ai-files so I saved it to eps but with the same result. I guess it´s got to have something to do with InDesign basic color presets but I can´t see that they are different in the two documents. Where´s the catch?
Do you have an identically named process color in your InDesign file? If so, delete it or rename it.
Also open the Ink manager (from the Swatches Panel menu) and check that convert spots to process is not checked.