Hey Ryan. It sounds like what you’re describing happened to me last week. The music coming from Deck B would be significantly higher than what was coming from Deck A using the same track. I tried it with the same song to make sure I wasn’t losing my mind.
To add insult to injury, it appeared the EQ settings on the mixer and Traktor were in sync, but it wasn’t until I turned each knob when the problem corrected itself. The LOW FILTER EQ seemed to have been the culprit because it was the last knob I turned when the sound came back fully.
Also, you may want to close out Traktor completely and re-open it to see if that corrects itself too.