I can't find significant differences between the SVG displayed in Inkscape 0.47 on OS X 10.5.8 and your attached PDF file (viewed with 'Preview.app', Apple's PDF viewer) - can you describe in more details what is wrong in the PDF or maybe create a montage of partial screenshots showing the differences on your system?
I can't find significant differences between the SVG displayed in Inkscape 0.47 on OS X 10.5.8 and your attached PDF file (viewed with 'Preview.app', Apple's PDF viewer) - can you describe in more details what is wrong in the PDF or maybe create a montage of partial screenshots showing the differences on your system?