I tried to reproduce the error using the editor in debug mode: create game with utility active and play a few turns and save. Exit game, exit utility. Then restart game and restart utility. Give myself enough money and technologies to upgrade and a unit that is upgradeble and upgrade it the same turn. No problem.
So I can't be sure what went wrong with my old game. I can't reproduce it.
But I can give you my savegame. If you start it and upgrade a unit in the same turn (don't click next turn) then the game will crash to the desktop. You'll need to loan some money from India to be able to upgrade (not cheap, got a bad reputation when some civ I was trading with got destroyed) and upgradeble units in cities with barracks are in the northern most island. If you go to the next turn, it will be no problem to upgrade units. The game won't crash.
If you would play a few more turns, exit the game and utility again and restart from this new savegame, the same problems will arise.
I can't be sure that it has something to do with your utility, but it is the first time in 1 1/2 years of playing Civ3 that the game crashed.
Note that it is a modded game, but the changes are only rule changes in the .bix file (I tried to make the game more difficult) and it didn't crash before and I can't reproduce it in debug mode of the editor.
I suspect this strange behaviour of this game will remain a mystery and it isn't that bad as I can work around the crashing of the game by not upgrading the turn I start the game.
Some other observations: With the huge modern age civs in this game of mine, we might be above the maximum number of units. Maybe that can give problems when I just loaded the game.
The savegame.
Maybe I gave to much detail here, but you asked for it.

Don't feel obligated to look into it. It might have nothing to do with your utility.