It's Dead Beat, and it's a biiiit more complicated than that, I think.

When Cowl was physically holding Bob, yes he had control of him. But Harry still seems to have priority ownership (likely because he got Bob through right of conquest when he killed Justin). The second Cowl let go of Bob, Bob was answering Harry's orders again.

Actually, it's also possible to interpret that scene as Bob playing double agent the entire time he's with Cowl, but I don't think that jives with the rest of the Bob canon...