@houaiss Just wanted to state this problem still exists. Apparently, the PDF should set the flag UserUnit. I haven't found a way to fix this in hind sight. The problem is that some PDF readers (most notable the Acrobat) are not able to read the file properly.
Many other viewers are perfectly able to read the PDF.
One source (this SO article) states, that this problem is even specific to Acrobat.
Either way, would be great if this was solved at the source of the PDF.