What actually controls the CD changer?

Another newbie question (and searched archive as best as I could)...

What actually controls my CD changer? The S-Link 0 output to my changer's CTL A1 input (this would be the obvious conclusion since it is a hard wire link)? Or(what is to me, because I don't see any doc about it) the mysterious IR rx 7/ IR tx 0 device/phone outlet with what appears to be a CAT5 wire? Or is it the IR rx 0 LED barely poking out of the Slink-E box?

I ask this fairly stupid question since, out of the box, everything worked like a charm. I had the Slink-E, my laptop and all the cables strewn about the livingroom. Then, when all the slots were identified and I had created some playlists, I wanted to clean things up a bit and moved my laptop and the Slink-E to the side of my changer instead of in front on the floor. Ever since, I've been have very erratic behavior, particularly with Playlists just stopping for no apparent reason or having the changer search endlessly for the next cd, select it, then re-select it then, and generally just seeming confused. This doesn't always happen, however, and it will go through the entire playlist without a hitch on other occasions (usually when I'm the only one in the room, of course)...