Thanks for the suggestion, Cleon.
Yes, when I deBayer a non-calibrated CR2 file, I get a dark image of the actual object. And this can be auto-stretched into something recognizable.
Here are some things I've tried over the last several hours of troubleshooting.
1. Stumbled on the fact that the Format Explorer/DSLR_RAW settings had gone back to factory default. Reset these, but it did not help.
2. Went back 3 times to the Calibration and Integration of the Dark frames before then continuing onto Light calibration, deBayer and then failing at Star Alignment (that is a lot of time).
My work flow is to create the Master Bias, Master Flat, Master Dark, and then calibrate them into my lights (images). I have successfully used the Master Bias and Master Flat on a previous image (did not change my setup). Currently, I'm collecting my Darks at the conclusion of the image session. So these and the Lights are what gets processed each time.
I had followed the same process with success on a previous object, so this has really got me stumped.
Mark