Also if you're like me, building from the top down (the top being the smallest probe, typically a lander with just a small omni), then the middle being the orbiter relay with a long range dish back to kerbin, I have to re-target connections, as after separation my giant kerbin relay in high polar orbit is then trying to communicate with the lander, not the orbital relay. The relay gets re-labeled automatically as a probe, rather than the other way around. That cost me a duna mission when I first started, before I figured out what it was doing each time.