I happened to note that if you pass a PDF through imagemagick's 'convert', convert it strips out the PDF Encrypted flag.
I needed to merge several PDF files into a single document, and using PDF::API2 this is really easy. This was until I found that someone had accidentally set the PDF Encrypted on some of the files when they were generated.
pdfinfo is the natty little tool which told me they were encrypted. Then convert sorted the problem out for me.
PDF can be very picky and quite a few generators actually get it wrong, I've seen one file which when printed through windows corrupted some of the very small text, but when sent via CUPs actually crashed the printer (so windoz was somehow correcting, reminded me of bad HTML and browsers 'correcting').
It was eventually tracked down to the pdf2ps part, which did give warnings, once they were fixed (upgrading Cario and switching to pnm images) printing from either windoz or CUPs was fine.
Having said that I no longer fear having to generate something as a PDF and actually would go so far as to enjoy using them.