I was working with a CMS and found that one file was not downloading correctly people were saying that the file was being zipped up by the CMS. Well it turns out it was the issue with IE6 and a bad MIME Type. The fix is simple for pptx you need the mime type application/vnd.openxmlformats-officedocument.presentationml.presentation once that was added everything was working correctly. With out this a PPTX file will download as a zip.
A few links on the subject: