Traktor glitching isnt a latency issue

I just tried to post this and it vanished so sorry if this is a double post. What happened is yesterday music i played through traktor pro 2 started making this glitchy popping noise when I play music. Mind you I run my audio through an S2 and everything is up to date and I hadnt changed any settings on my computer. I simply turned it on expecting it to work as it did earlier in the morning but noooooo. After hearing of many other people with this problem as a latency issue I proceeded to change every setting in my traktor and on my computer to optimize performance. After that didn't change anything I went to a third party latency analyzer which showed that my computers latency was minimal and shouldnt be a problem playing live audio. Here's the kicker, I have all sound on my computer running through the S2 (youtube, itunes, etc.) and all of that audio plays perfectly fine. ANY HELP AT ALL WOULD BE AMAZING.