Change their team to something else appropriate and add the allegiance function to your script, see if that fixes it. I'm pretty sure broken allegiances are a team-to-team thing, and not unit-to-unit.
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Bungie used a feature called "recorded animations" to re-play a dropship being driven in and then flying out, with the script unloading the dropship in-between those animations. This feature has been rendered useless in the public version of Sapien, as Sapien does not accept player control input; this is needed so the game has animations to record.
The only other ways I could think of would be to get an AI to pilot the dropship, and then use command lists to direct it, or to actually animate the dropship in 3dsmax.
No, that's because HEK+ didn't rip them right.
It just plain doesn't rip right. I don't know why the people who have ripped them right haven't released them in a pack or something.
Try the older HEK+.