I generally used puppet mode for better control of combat. As far as I remember this did not stop companions obeying Follow Me and Stand Your Ground etc.

In one save game that I went back to I found that none of these commands have any effect. I have to move each character individually. Is there something that I'm missing? I've closed down the game and restarted several times.

Is this a NWN2 issue?

Yes, it is

EDIT: The "Following" message appears above my char and Khelgar's heads, but no action happens. Neeshka joined recently, and she Follows either one of us when asked, or any other action.

I can't play without Tony's AI! This setting fixed it, thanks!

It is about two thirds down the list, where the other puppet mode settings (individual) are at the top which is how I missed it.