When you output a file for printing on a conventional press, whether it be an offset press, a flexographic press or a rotogravure press, you need to "separate" the job into its cyan, magenta, yellow, black (we call it CMYK) and "fifth" colors. (A fifth color might be something like PANTONE 871, which is a metallic, as are all the 870-series PANTONE colors - it has metal particles in it as its pigment. If you want the printed piece to have a stripe of gold, silver or bronze in it, you put out a sheet of film or a plate for that color and load that ink into one of the towers on your press.)
If you use a professional-grade layout program like Adobe InDesign or QuarkXPress, it works in CMYK internally. If you put a process color like 100%C, 44%M, 0%Y and 0%K in your job, when your film or plates come out of the imager the cyan channel will have a place with 100% cyan and the magenta channel will have the same place with 44% magenta. In case you're wondering, this is the build for PANTONE 300, a really pretty blue. This goes whether you're running separations straight out of the program to your imager or putting out a "composite" PostScript or PDF file and laying out the plate in an imposition program like Preps, which arranges the pages so that when you fold the printed sheet all the pages are in the right order.
Microsoft Publisher works with RGB data internally. To get it to separate you have to run it through the Windows print driver, which uses Windows' color management system to separate it into RGB.
"Well, that's not so bad. You can just strip in the film for the Publisher files." It is if you're running an imposed workflow - especially if not all the pages in the job came out of Publisher. I have personally ran jobs built in five different programs - some in Publisher, some in Quark, others in an Adobe layout program, then CorelDraw and Aldus FreeHand. And that doesn't work at all if you're running a direct-to-plate system like everyone does now. Modern digital front ends can separate RGB to CMYK, but you're almost guaranteed to get colors different from the designer's intent - especially RGB blue.
There are two problems with putting a CMYK engine in Microsoft Publisher. One is that most people don't need it - if your output device is an $89 desktop inkjet printer it's not going to support CMYK input, and that's the typical output device for Publisher. The other is the CMYK engine would probably triple the price of the program, and the only positive attribute of Publisher is it's dirt cheap.
And so, I am quite glad that those files will soon not be entering prepress professionals' nightmares.