Weird spots in rendering result of scanned PDF 1.6 document

The rendering of some scanned Documents in PDF 1.6 format result shows weired blurred black spots. It seems to me that the scanning software detects form areas and moves them in separate elements, which are not rendered by PDFBox. The result in Adobe Reader and other conversion tools like Image Magick (which is using ghostscript as PDF renderer) is absolute perfect. Besides the mentioned spots, there are some other rendering bugs resulting of wrong positioning of the graphical elements of the PDF.