I went through this for a long time. There are a LOT of addons that have nothing to do with your action bars that can cause this issue. You could disable one by one and figure it out, but in the end, I gave up using the default Blizzard action bars and installed Bongos2. Now I always see the pet action bar, whether I am Mind Controlling, using Shadowfiend, or playing Chess in Karazhan.