Ok, I manage to get it to work,
i found it was reporting a ntlmsso_iwamagicnotenabled error, found one reference on the moodle site for troubleshooting but i passed that ok.
What i did find was that with debugging turned on errors are written to the PHP Log files, from there i was able to discover that the the UserName Format was incorrect.
So i corrected that and then it worked, I did come across a few things though,
the error ntlmsso_iwamagicnotenabled can be set if either the ntlmsso_magic function fails or the file spacer.gif is not avilable. this does not make sense as the image file is required only if IE Fast Switch is not available. So i adjust my code to reflect this.
Also i did notice that when it does fails on SSO neither the continue or login links would work so i could not get on regardless.