Finally got it working. Thanks everyone.
One thing I noticed is the sidewinders holographic displays were illuminous, as were all lights in the cockpit.
I changed the brightness in the Option->Graphics menu, and while this did reduce the brightness the colours were still day glow orange, like contrast was set to 100%.
When I was looking around the cockpit I moved my head outside of the OR tracker sat on my monitor. As soon as I went outside the tracking range all colours in the cockpit turned normal. No day glow this time, but instead normal soft colours, the same as when playing on my monitor. When I brought my head back into tracking range...*poooof* day glow neon colours again.
Asteroid etc all look fine...it's purely the holographics and lights.
I raised a thread here about it and will raise a ticket:
http://forums.frontier.co.uk/showthread.php?t=28832