Well these weren't the Founders technically, these were renegade Changelings disconnected from the Great Link. But I agree, I don't understand why the Changelings would work for the Borg other than they didn't know they were working for the Borg. I wonder if all those Changelings impersonating officers got killed off in the takeover.
Well Vadic certainly knew. She was taking orders from them, knew Jack was connected to the Borg, and knew what he was going to be used for (so presumably she was going to deliver him to the cube). The changelings also presumably knew what they were doing with the transporters.