Strange thing. The Denon devices are known to have slight problems with high frequency reproduction, but I have never noticed what you are describing - especially in comparison to Traktor, I always thought that Traktor sounded worse than my SC6000 (Traktor doesn’t necessarily have great sound either).
Do you have any effect open in Traktor? Is the SC5000 up to date with the latest updates? Could you possibly record a sound comparison?