Based on your description, I assume you are running on a Windows system with both Office and Acrobat installed.
There are three ways of producing PDF from PowerPoint in this situation.
The first method is to use the Save as Adobe PDF / PDFMaker solution that doesn't involve printing at all. It produces the highest quality PDF of all three methods, but the options for this allow the notes only to come out as PDF annotations in a separate,hide-able layer, not as the full Notes Pages format, regardless of the current settings for displaying the PowerPoint file on screen. You can see the annotations in comments pane in the comments tool. This isn't what you want.
The second method is to use the Microsoft Save as function and specify PDF instead of a .PPT or .PPTX file. If you press Options, one of the options is to publish the Notes Pages instead of just the Slides. That will give you what you want, but Microsoft's generated PDF is somewhat wonky, often generating invalid PDF with improper font references and other problems too numerous to get into here.
The third method is to print to the Adobe PDF PostScript printer driver instance. The secret here is that under Settings, instead of selecting the default Print All Slides, you need to select Notes Pages. In other words, the print function ignores the view you currently have on the screen. The only problem with this approach is that the resultant PDF file is not nearly as high a quality as the PDF produced by Save as Adobe PDF, but it should probably be sufficient for your needs.
That having been said, I will submit a request internally to “beef up” our Save as Adobe PDF to provide an option for the Notes Pages as an alternative to putting out the notes as annotations.
Please advise if this solves your issue.
- Dov