Hi Pierre,
What does the coma look like in a single sub? If it's reasonably circular, then the hourglass shape could be a dithering issue. If you dither, the CometAlignment process can't exactly register the comet. In my case it came close, but I used the DynamicAlignment process to tweak the subs after CometAlignment (one sub at a time).
You can use the Blink tool to look at the subs after CometAlignment and see if the coma is well registered or not.
Don