This seems to be happening for me with anybody that I remove from my party and then add back to it. It's currently happening on Aloth, Tekehu, and Serafen. But everyone I've kept in my party constantly (Eder, Xoti, Maia) seems to be working fine. I haven't tested this really so it's only an observation/hunch on my part. Might have something to do with your inactive party members getting a different AI package when they fight in the ship boarding battles, or something?