That is interesting. I have the exact same problem. Tried to save it to the desktop and it saved to my home directory.On the second try I typed in the directory that I wanted to save the file. Instead of "output.pdf", I put "/home/ill/Desktop/output.pdf".
When I try to print to PDF with evince or firefox it will not print pdf file to a directory I specify only to my home directory.
Does anybody know what to look for? It just happen after recent upgrade.