The problem was traced to the Darks I was using. I had been shooting with the colour camera earlier this week, and mistakenly picked up the colour camera Darks to stack with the Mono lights in DSS. DSS doesn't make it easier, as it uses the same file naming convention, and as the subs were the same length and shot at the same ISO, it was easy to grab the wrong ones. I have now separated all the colour and mono camera files so hopefully it will not happen again. It would never had been an issue if I was not using two cameras so similiar, but so different.
If your confused about why they would be different in two Canon 450D, its because the debayered mono sensor has artifacts of the debayering process that need to be processed out and DSS does this with column repair and hot pixel elimination. Using Darks from the colour sensor it misses the artifacts and treats them as signal.
THanks to all that offered advice and assistance.
Here is the resulting test downsized for Astrobin:
http://www.astrobin.com/full/244873/0/