Please use Windows to view Adobe Presenter output.
Flash content cannot be played back on MAC
Well, that isn't true. Flash content plays fine on a Mac, but not in iOS devices.
That said, you should check the version of Presenter that output the PDF's, and go to 7.0.6 or 7.0.7 if it is not there. There were many bug fixes up to 7.0.6 so it could have been one of the issues with an early version of Presenter.