Thanks a lot for your reply Greg, extremely helpful
I'll give a more detailed description of what I did, so I got the camera going around 6 o'clock (my cooled, modded 350d) and after about half an hour (to let it cool down) I started capturing darks. Then around 9 o'clock framed and focused and started imaging. I imaged all night and in the morning when the sky had brightened and I couldn't see any more stars I took the flats. I didn't touch the camera (left it pointing at the sky) beyond changing the exposure to 1/200 and the iso to four hundred. The histogram was about 2/3 of the way up so that may have been a problem?
The camera would have sat on around -8 most of the night I think.
All the darks and bias frames were stacked with a pure average and the flats with a 2x2 median (what ever that is, it's what Nebulosity recommended)
I removed the bias from the flats, and the darks and flats from the lights.
I'm not sure if Nebulosity has a clip max/min combine but it can do a standard deviation stack which I think chucks out any pixel thats over a certain value, would that be similar you reckon?
The dust is mainly on my sensor thats why it's so big and dark.
Cheers and thanks again
Jo