What version of Power Point are you using? I experienced the same issue publishing from a pptx file in PP 2007. If I save the PP file to a ppt and then published everything was fine....
I tried your suggestion and my computer just hated it! Would not let me do it. I'm using Office 2007 on a ThinkPad. I did figure out that Presenter 7 liked the 2007 PPT templates, so I recreated my PPT in a 2007 revised template. Then I imported sound from a previous version and eventually got a beautiful published presentation. Took way longer than I had hoped though.
Thanks for weighing in!