I assume you are bringing in your charts as images. If so, you are experiencing expected behavior. You can test this without involving NPrinting at all. Simply export your chart and save it as a PNG image directly from your QlikView document. Use this image in a PowerPoint slide and try to manipulate it's background transparency. In my tests I was not able to make any changes. NPrinting uses the QlikView API to export charts as images so you can expect the same behavior.
Have you tried creating PowerPoint charts using native QlikView tables instead? You have more control over transparency this way.
HTH - Daniel.