That could be it.
I plug in the mk4, wait til the light comes on, launch traktor, load the tsi file, and I checked the input and outputs in the traktor preferences, and it only shows "Line in 0" and "Line in 1" as my options. It should be Input 1, 2, 3, 4, and Output 1, 2, 3, and 4, right?
Not sure why it's doing this.
As for the tsi file, it's named "TP_DJ_Mk4(PC)_v1.24.tsi" so I think it's the right one.
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I fixed this by selecting a different audio device, but now the same problem persists. Moving knobs and sliders on the mk4 does the correct movements in the software but it also moved something completely different and makes using it impossible.

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"As described in the instructions provided by Hercules, the MIDI In and Out need to be assigned correctly to the profile you want to use. If the MK4 MIDI In is also applied to other profile, that could explain the interferences..."
what do you mean by this? How to I check to see it's only applying the TSI I want and not more than one?