I've also noted that on a reload, your civilization seems to stall for a turn. I know this isn't scientific, but I wanted to add my two cents.

No, it's a myth that the game is designed that way. The developers have confirmed that this is on their bug-list.

i hope they fix this as it severely messes up the games where I can only play for a few minutes at a time.

In my last game things changed rather dramatically because of this, I think.

I was allied to several races, the only one not was the Drengin. They had just declared war on the Iconian Refuge, which then asked if I would honor my alliance with them. I said yes, which put me at war with the Drengin. I had just been building a new set of ships, as the Drengin were the only race aside from myself with beam weapons and I needed ships with shields for this war. So I brought out my new ships on the next turn and started the removal process of the Drengin ships.

During the next turn, after I had wiped out several of the Drengin ships, the game crashed. No biggie, I thought, just reload the autosave and redo the last few turns. My autosave is set for 5 turns.

When I came back in, the Drengin were at war with the Iconian, but I never recieved the message asking for my help. I was not at war with them either, yet. So it seems that the game was saved on the turn that I was asked to honor the alliance, and when I reloaded that step was skipped.

So the difference is that I now had to declare war directly on the Drengin if I were to help the Iconians.
I decided to contact the Drengin and tell them to stop their war on the Iconian. The Meese always give at least one chance before pouncing, don't you know.
And, they did, no questions asked. I just said, Make Peace, and they said, OK, you owe us a favor, and the war stopped without a shot being fired from anyone.

I won an alliance victory the next turn because the Drengin were then close and I allied with them as well.

So I never got to use my new fleet of ships after all. Oh well. Win some, lose some.