Okay I have three bugs with Dark Avatar.  Forgive me for placing them all in one thread.

First, I play the game at the Painful level with 5 randomly selected opponents and Randomize Intelligence OFF.  In about one game in 20, I'll play a while before discovering that the 5 AI civs are not expanding.  One time when this happened I looked at the stats for the other races in the game, and found all of their intelligence was at the lowest possible level.  Keep in mind I was playing the game in Painful without randomized intelligence.  If I select the opponents instead of random selection, this error never seems to occur.

Second, There have been many times where I used the governers to order all colonies to send all their new ships to a certain rally point (which is clearly in range of all the planets in question).  There are almost always a few planets who refuse to do so, even though they launch the ships automatically.  Once launched, the ships just sit next to the planet and await orders.  If those planets had not been included in the destination order, the ships wouldn't have launched.  Re-assigning the colony destinations does not fix the problem.

Third, If I have a custom ship saved to my hard drive, then upgrade it and save it with the same ship name and description, the saved ship reverts to how it was before the upgrade.  This usually happens when the upgraded ship has the exact same equipment as the previously saved one (like, I open it, change the position of one of the weapons, and save it.  When I look at it after the save, the weapon is back in it's old position).