My hope is that Lord Brazen or someone can use this to find that crash/freeze bug and fix it.
I wrote a little readme which says what I've observed about it, and how to get it to crash. Although I've included it in the zip, I'll also paste it here for convenience:
Combat crash/freeze bug demonstration save
This saved game is 1 turn from a defensive combat which, (if you don't attack the enemy fleet before they attack one of your colonies), consistantly crashes or freezes (usually near the end of the combat, when the enemy has around 6 ships left) with 1.40b22. It froze the first two times I played it on manual control, and crashed the next six or so times I tried it on auto. (But then I tried 1.31 and it didn't crash, and then I tried 1.40b22 again but preemptively attacked the enemy fleet before they could approach a colony, and it didn't crash/freeze then either.)
So, to have the bug happen, just do this:
1. Load the game (save #3)
2. Hit the 'next turn' button
3. If you're using 1.40b22 you should get a popup asking you where you want to have combat. Click cancel. (If you're using 1.31 this doesn't seem to come up)
4. The enemy should attack one of the colonies, and you should have a large fleet against their large fleet. They seem to like attacking Atlantis II, but I didn't check to see if they attacked the same colony each time.
5. Turn on auto combat and let the battle go. It usually freezes for me when the enemy is down to 6 or so ships. Sometimes it dies during the enemy's turn, and sometimes it dies during mine.