The highest ranked officer should be the Task Force C.O., but Aurora doesn't check the whole T.F. when you add a new ship. Try removing the ship the current C.O. is on and hopefully it will check all the current officers to find the new highest rank. If not, then it is probably going by order of 'date added to T.F.' and you might have to cycle ships in and out until the C.O. you want is the one who's been in the group the longest.
Also, I may have typed 'Task Force' when I meant 'Task Group' and vice versa through this whole post.