PDF (created in Indesign CS4) separates in CMYK, in stead of PMS

I have sent a PDF, created in Indesign CS4, to the printer. I need the design to be printed in PMS colors, but the printer says the PDF color separates in CMYK, not PMS colors.
I'm at my wits end trying to find where I went wrong (I should add I'm a beginner at all this). I need help...
Here's what I did:
I have changed the colors in a CMYK based design of a business card to PMS colors. I have changed the colors of an Illustrator file that is used in the design to PMS colors as well.
When I look at the separations preview it looks fine, only PMS colors.
I then created a PDF, using the [High Quality Print] Adobe PDF preset. In Output Color Conversion is set to 'No Color Conversion'. In the Ink Manager 'All spots to process' is not checked. CMYK inks are visible in the Ink Manager, but so are the Pantone Inks I used.
I noticed one strange thing, the swatch options for Pantone Process Cyan C are different thatn those in other PMS colors, the Colortype is 'spot' but the Color Mode is CMYK, greyed out so that I can't change it to Pantone Solid Coated. Even weirder, I can't delete that strange swatch. I tried adding the pantone colors to my swatches again, in a different file, I added Pantone Cyan C and it looked fine, but when I reopened the swatch options it was strange again.

Yes, I have added cropmarks and page info to the pdf.
I checked the separations in Acrobat Pro with a friend. Both Pantone colors and CMYK show up. When I disable the CMYK, nothing of the design disappears (cropmarks and page info don't disappear either, they seem to be in both Pantone and CMYK).
I saved a new pdf, without crops and page info, and CMYK still shows up in the separations.
I'll contact the printer tomorrow, I'm pretty sure he should be able to use the file I sent him.
Thank you all for your help!

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