If you keep your Windows/Office updated there should be no problems with Powerpoint/PPT files.
Further information you will find at this FAQ article:
http://www.provisio.com/en-US/CustomerSupportCenter/ArticleDetails.aspx?ArticleID=457
If you still have problems with using PPT / PPS files you can convert the Powerpoint-application into an HTML-presentation by using Office (Powerpoint). After that, simply embed the HTML Start Page of the HTML PPT presentation (usually fullscreen.htm) into the configuration.