OK, this really stumped me until I did a bit of searching and found some really useful posts which I have listed below.
The documentation in the infocenter tells you to copy true type fonts to the Linux server and set a number of paths:
After adding the paths ensuring the paths were set permanently documents still wouldn’t convert. Reading the links below I found that I also had to add a path for Java to run, I used “/opt/IBM/WebSphere/AppServer/java/jre/bin” since it was installed with WAS. It would be nice if IBM updated their documentation.