... Open Adobe Acrobat and use Create PDF From File, feeding it the Powerpoint file to convert. See if that does the trick for you.
The Save As function never has been real reliable. So, printing the presentation first will often reveal any problems that are going to be present when saved as a PDF. If it doesn't print right, it won't save as right.
To explain... 'fly in' is a term used to make text appear to move into place as it shows up on the slide while showing the presentation.
A PDF writer is another program, such as CutePDF, which creates a virtual 'printer'. To create PDFs, you simply print your presentation to that specific printer and it saves it as a PDF file instead, using an image of what would have been printed had it been a real printer. This saves having to buy Adobe Acrobat just to have the ability to create PDFs from other types of documents. Of course, without Adobe, you can't edit the PDFs.