I have tried a lot of complicated fixes with colour setings over the years, the simplest and quickest solution for print jobs our our shop is as follows;
Convert everything to Adobe Acrobat, save the whole file as normal in colour.
Save the same file in Acrobat using save as and tiff, the whole file as greyscale tiffs. (check the quality)
Open the first Tiff page - Usually numbered as **01.tiff - use the command File-combine-merge files into a single tiff, add all the seperate tiffs in, combine and this gives you a greyscale pdf.
Open the colour PDF and the greyscale pdf side by side on the screen, drag the colour thumnails you need from one greyscale side into the colour side. Delete the thumbnails you don't want. Voila, a combined colour & Greyscale document, easy and quick for things like Word files etc.
The only other thing to keep an eye on is in the File-Print-Advanced-Colour Handling section, there are 3 options, try each one if you have a problem. Chris