Er, would be nice to know what you are using to print the file. Those colors are Pantone Spot Colors and will be interpreted by whatever print driver you happen to be using. Or, yes they will default to a Red and a Blue. FilemakerPro is not exactly the defacto standard for print publishing. Distiller converts your file to PDF using default settings or custom settings you create. Acrobat has some control, but all this really depends on your output device and, to go a bit further, your paper. What did they say in the Filemaker forum?
I'm not even sure what printer we use since we send the PDFs out to be printed on a glossy paper (I'm new to the position so I don't have all the details yet). All I use is my Adobe PDF printer. I'm also not using FileMaker, I'm using FrameMaker since I am producing manuals that will be printed, not marketing material or anything with a lot of images. I am just trying to get the logo colors to appear correctly in the PDF so that when it does get printed off-site, the Pantone colors are seen and not the default in the final product. I will post this in the FrameMaker forum as well.
Thanks for your response.