If your MIDI-controller is working fine with the exception of the effects sections in TRAKTOR, the FX Panels (FX Unit) may be set to the wrong mode. There are two FX Panel Modes for the effects in TRAKTOR PRO 2: Group and Single. Both of these modes require different controller mappings. The FX Panel Mode needs to match the one selected in the controller mapping, or otherwise the effects can not be controlled. You can switch between the FX Panel Modes under Preferences > Effects > FX Panel Mode. Select the alternate mode for the FX Panels which are not working with your controller.
Note: If you want to use a different FX Panel Mode than the one your Controller is mapped to, you need to modify the device mapping in TRAKTOR`s Controller Manager. For further information, please refer to the article How to use the Controller Manager in TRAKTOR.