I can't toggle companion abilities on and off. It hasn't always been like this. It began about a week ago with one of their patches. I was really expecting them to fix the problem today but it still exists and is especially annoying when your companion is constantly breaking CC because you can't turn their AOE off.
I found that problem recently too when I wanted Kaliyo to stop charging mobs (I wanted to do it manually only at the start of combat, so it's always off CD when pulling packs) but I assumed that my use of it manually was also turning it on for auto use. Someone, though, has said elsewhere that their companion has been resetting as you describe every time he mounts/dismiss/send on crew skill.
If they are the same bug, then I imagine that they are easily reproducable and are being worked on.