Thanks for the replies guys
brent
The Java side is fine, the bank used to enforce using Oracle Java but either IcedTeas has changed something their side or the bank have taken the stick out of their ass as I can now run the app on IceadTea and OpenJDK instead of setting up Oracle Java.
Justin
Yes, I can open them in evince. I had realized that, but I was so busy looking for an "export" or "save as" to PDF option that I totally forgot that I can print to PDF from evince.
So it's a bit roundabout, but I'm now using the print to file, to PS, opening that in evince and then printint that to PDF and editing that file then.
Should there be a better way someone can come up with, please let me know.