We had this problem, but it was because of the font selected to generate the pdf, it was not between the fonts installed on the Linux server, and when generating the PDF with the default font it had a problem with non English characters. It might not be your problem, but it's worth checking. Take a look to the fonts installed in the server and check if the font you're using in the report is one of them. If not, test quickly if that would solve your problem by doing a quick report using one of the fonts in the server.
Regards
OS: Ubuntu 16.04 64 bits
Java: Openjdk 1.8.0_131
Pentaho 6.1 CE