If you RMB on your chart in your QlikView document and then select Copy to Clipboard > Image (or Export and select an image type) and check the result, you will find that the background transparency is not retained. QlikView NPrinting uses the QlikView Desktop API to render the chart images so you get the same result.
PixelPerfect has a huge range of chart types available - perhaps you could build them there? If you do, you will have a lot more control over chart properties. For example this screenshot shows background transparency:
You will find links to all PixelPerfect tutorials from this starting point: QlikView NPrinting 16 Tutorials - PixelPerfect Reports
HTH - Daniel.