If you ever have an error printing from a java based program that looks something like this:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException: null attribute matlab
and continues on, then do this:

Specify the page orientation of every printer in cups

System -> Printing

For each printer select Job Options tab and specify Orientation to whatever else instead of "Automatic Rotation".

Thanks to trinh in ubuntu launchpad for the tip above.