I find it distressing....

[DirectorTsaarx]

It may be that you had too many ships in the first battle. I recently watched a battle where I had about 30 fighter Groups, plus a dozen ships, trying to attack a planet. It appeared that the computer had trouble moving all those fighter Groups within range of the planet; rather than spreading them all around, they all got concentrated over one "corner", and a couple of the Groups stayed out of range for a while. Now, some Groups moved away because they had 2-turn reload times (planetary napalm or whatever the fighter equivalent is), but some just couldn't get closer because there wasn't any maneuvering room. The ships were OK because they had much longer range, but even then the ships sometimes bumped into each other.

I imagine the same thing could occur with 100 ships; especially if they were treated as one big fleet. Imagine trying to maintain formation with 100 ships! And if your leader was a missile boat, it may have kept trying to run away for two turns out of every three while the missiles reloaded.

BTW - only two shield generators on a dreadnought? I usually try to have three, maybe four on large (BB, DN) beam ships. And I'll generally put two on each cruiser. On basehips, I'll put four or five shield generators. But I also tend to build small fleets, so I can't afford to lose many ships.