Mixcraft 5 doesn't have control surface support. Is that what you're using? If so, try Mixcraft 6.
If you're already using Mixcraft 6, here are some suggestions:
If you're using a USB hub, try bypassing that and going directly into a USB port on your computer If you're not using a hub, just try a different USB port. Make sure you don't have any other MIDI applications open when you launch Mixcraft and also that your Nanokontrol 2 is recognized by Windows before you start Mixcraft.
You can also try installing the Korg USB-MIDI driver from the Nano Series driver downloads page
Note: you can only use the faders to control the selected track. You can't control all the tracks simultaneously.