When a pdf file has a shape that is drawn with a transparency value the transparency values are not respected when exported to image.
I have attached a small patch that fixes this issue. The patch does not fully satisfy the PDF transparency model, for example only Alpha composition is used. But it covers the most common use-case of drawing shapes with a transparency value for fill and stroke.
I have also attached a maven project that demonstrates the issue. It had a pdf with a shape in it that is semi transparent. Running the application (execute the runexample.sh script) will load that pdf and export it as an image. During the export (the output is a file called pdfAsImage) the transparency is lost.
Compare the exported image and the original pdf to see the difference. PDF is in src/main/resources/...