I finally fixed this behavior by changing the following line 418 of the unmodified X3 AP Director file 0.1 Assassinate 1.xml
FROM
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<set_actor_location actor="{param@Cue}.{param@ID} L0Mark" object="this.Target" location="pilot"/>
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<set_actor_location actor="{param@Cue}.{param@ID} L0Mark" object="this.Target" location="crew"/>
For some reason my game was freaking out and the ship was stuck unmoving if the "{param@Cue}.{param@ID} L0Mark" and the "{param@Cue}.{param@ID} L0Target" where both the pilot at one point in a bailable ship.
Just thought I would post this in case someone else has run into this issue.
PS : I just realized that I think this is the same fix dillpickle uses to force people to have to actually kill the targets on bail. Behavior is the same as his mod.
For reference
http://forum.egosoft.com/viewtopic.php?t=324236
PS2: Nope not the same fix after looking at it, but the same effect of having to kill a bail, at least a forced bail. Though I think they would have the same results.