Problem:Users would launch JAVA the first time on a windows 2008 box
They have a roaming profile configured
The application would launch first time – without issue
They would log off
After the user logs off (and the ntuser.dat gets updated)
Java would no longer launch for anything / no control panel / no apps / no .jar files opening (regardless of java version)

Solution:Apparently there is an issue with JAVA and the Clear type / font stuff on windows 2008.
Deleting the users HKCUControl PanelDesktop registry settings – (on logon with script) > results in the java apps working everytime.