Okay, steps 1-8 add up to a bug in setting a bot's custom colors. Bascially, if bot had a custom color, the act of clicking on it would reset that color to green. Has to do with the way the options dialog refreshed itself when a species was selected. Bascailly, the species color dropdown click event was geting fired with the wrong color for the selected species, effectively resetting it if the color was custom. This bug may be as old as the hills - not sure how many people actually use custom colors - but in any event, it is fixed in 2.43m.
I cannot reproduce #9. Are you absolutely postitive it is running the lastexit.sim and not just a new sim with the wrong bot colors?