Hi bluemax,
Recently I was very lucky to get Atik 428EX for testing, and it happened that I also use Nebulosity for image acquisition.
I had this camera for about two (very short) weeks and never had any problems with Nebulosity controlling it. Once I run 250 short subs in a row (bias frames) and also a number of flats, twice had enough time to run 30 subs 300 seconds each (narrowband), also once 50 subs 60 seconds each. Had the camera connected via ASCOM drivers.
However, as I remember, once I got a similar message when using a small Orion G3 camera, but later I updated ASCOM drivers for this camera to the latest version and had no problems with Nebulosity since.
Have you tried running imaging sessions with the provided (Atik) software?
Hope you will resolve your problem quickly.