If it's in the mission editor, then it might be because of the entry/exit dates. Left-click on the Aux.Cruiser icon, and then right-click and select properties. Look at the entry/exit dates of the ship. If your mission is set to start outside of this time-range, you should not expect this ship to participate (i.e. it won't move in the mission editor simulator and it will not appear in the mission itself.)
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