Well l have just discovered the solution,it turns out jscalibrator doesn't exit cleanly.The result being if you run
another application straight afterwards-the buttons work;BUT NOT THE AXIS!!!!.
Here is the url to this gem of info; http://gentoo-wiki.com/HOWTO_joystick_setup
And this is the specific portion of relevant text;
Picky Programs / buggy tools
If you run another program after jscalibrator you will probably only see the buttons working. Reloading the driver module should correct this and games such as gl-117 have the jockstick calibrated because of the ~/.joystick file created by jscalibrator.
This is a bug in jscalibrator which does not exit cleanly. It leaves large offsets on the axes so that the mouse pointer is permanently off-screen. It is sufficient to unload the sound card module
modprobe -r <modulename>
then reload it as before. We dont like rebooting Linux.
Now l have run jsconfigurator as a check BEFORE trying the games-thus my problem.
Hope this helps others who use jsconfigurator.