First question - just HOW are you making the PDF?
There are two ways of making a PDF from PM (and many other apps for that matter):
(1) Export direct to PDF
(2) 'print' a postscript file and then distill it.
When I used Pagemaker, I would always use the second method, as I found it more reliable. But others have used the direct export without problems.
Either way, you have to be careful which job options you choose to get the desired results. Without knowing which version of PM and Distiller/Acrobat you have, it's difficult to be specific.
But if you have at least V5 of Distiiler, then there are pre-set job options to choose from. Depending on the destination of the PDF (press, inhouse printing or the web), will determine the best job options to choose.
If your PM colours are converting to greyscale, this usually indicates you are using method (2) to make the PDF and in the first step, you are choosing a mono postscript printer (black not a colour printer).
When you create the postscript file, try using Distiler as the target printer.