I found and ran this dead pixel dedection software.
StarZen Technologies, Inc; DataFlex tools and books
It only found 53 dead pixels at 30 seconds and 0 at 1 second at ISO 400, which Probably is not out of line, but the problems showing in the images are in the thousands. I'm at a dead loss as to what is occuring.
I have tried different ISOs, and different lenses, and different shutter speeds, and the bad spots stay in the same place.
One of the side effects is that the images allways appear "muddy".