Hi!
This is a hard one to help you with as there is so many things that this can depend on.
It could be that the club mixer and PA equalizer is set to that amount of bass (I think that is the case)
Or that they have different amps for tops and bass and that they are wrongly set up.
You should lower the master volume in Traktor to 1/1 -> 3/4 and higher the volume on the S4 mixer
after setting the channel volume to about 0db. and then set the club mixer after that so that you get whatever volume you want. You should never run on red!!!!!!
I hope that this is of help.
If not I do think you should adress this to the Native Instruments forum
because they have more knowlage about your specific gear.