Korg stuff is nice but it's a pain to get set up. However there is not enough info to work with in the OP. You need to a) read the X3 manual entries on setting up your devices, b) how to set up tracks to accept signals from an external controller, c) make sure you read the documentation for the nanoKontrol to see if it has any special weirdness you have to do to make it work normally. Korg documentation is kind of weird.
If you've done all that describe, step by step, exactly how you hooked it up.
Some other thoughts...
Make sure you have the latest drivers for the device from Korg's site and always/only use the USB port you installed it on. If I move my padKontrol to another USB port than the one I installed it on things can get weird.
You say it is showing up in your devices list in preferences but it also has to be selected (checkmark beside all the Korg entries in preferences).
Sometimes untinstalling and reinstalling the drivers will shake something loose (and remember which port you used to install it and always use that port for the device).
Make sure your track has MIDI Echo enabled.
Oh... and welcome to the forum. ;-)