Buff responded "Perhaps try posting in Third Wire's forum for the other issues - afaik you are the only user to report this."
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He's not the only one, I too have the same problem. I downloaded and installed Service Pack 3, Update 3.1, and 3.2 in order. However when I hit the fly button in instant mission mode it crashes to the desktop. I didn't seem to have this problem after installing version 3.1, just 3.2. I'll try reinstalling it again, this time by also reinstalling the Direct X 9 as well.
In case you're wondering I'm running XP with an Intel graphics.