Thank you Bruce,
I am not a specialist for the configuration and a specialist told me :
Hey Bernard,
Having been unable to get this working for you I've highlighted the issue to the Technical Support manager. Unfortunately setting up and maintaining this script/application falls outside the scope of our support for a dedicated or virtual dedicated server.
I've tried tweaking the Tomcat timeout values and some other timeout related settings and the error is still happening.
In addition to this I've setup Xterm and tried to link this to the install and again it doesn't appear to have resolved the issue.
Due to the nature of the application I'd suggest possibly hiring a WebMathematica expert to look into this setup.
Thank you,