I also was wondering about this. I was so happy w/ the sound of my system I was a bit paranoid about compromising sound by splitting the signal. I'm sure splitting in itself should have next to 0 effect but one of my runs was going to be much longer than the other and w/ a different type of interconnect and going to an HT amp w/ unknown input impedance characteristics. I decided that rather than risk allowing interference in from the long run (27'), I'd buy a switch to take the unused cable out of the circuit completely. Head-Fier Fiddler makes a nice looking passive switch and I've got one on order. His cables also look nice so I ordered some of those too! I'd try it to see if you hear a difference; otherwise a switch like Fiddler's might help.
CPW
CPW