Gonkboy.
You really need to carefully read the manual for your S2 and for Traktor pro IMO.
Then I suggest you get a copy of the Traktor bible.
After that you can start using the S2………
That way you will get the most out of your equipment and software and you would not have to be upset by such things you just did.
Your problem will accor again if you start Traktor before the S2 is connected and started because then Traktor will not find your S2 soundcard and therefore it will chose the internal soundcard of your PC.
//DJ Hessler