OK, I played the first battle over & didn't learn anything new. But while playing the rest of the Ori battles I noticed the same thing. The Ori motherships seem to always get damaged in their rear armor/shields much too quickly. It was when I heard that 'klaxon' sound used for ships blowing up and couldn't find anything blowing up that I realized what was going on. When the Ori motherships launch fighters, they aren't moving fast enough for the fighters to clear and they hit and damage the mothership. And that's why the klaxons were sounding all the time. Ori fighters getting destroyed on launch. It was the regeneration powers of the armor replacing the rear shields that made it harder to figure out what was going on.
This might be another problem caused by my using a slower computer, or it might be something you can see for yourself. Either way, I wonder if there is a way to adjust where launched fighters appear? Is there a 'launch point' just like there is a 'firing point' for a weapon?