The System NX Directory is the directory from where the nxclient executable is run, i.e. C:\Program Files\NX Client for Windows on Windows or /usr/NX/bin on unix-based  O.S.  The User NX Directory is the directory where the .nx directory is located, by default it is the user's home.

When NX client starts, it retrieves the location of the System NX Directory and the User NX Directory by getting the values of the corresponding items from the nxclient.cfg file.

NX Client uses the following search paths to retrieve the nxclient.cfg:

   1. System NX Directory/.nx/config/nxclient.cfg
   2. User NX Directory/config/nxclient.cfg
   3. /usr/NX/etc/nxclient.cfg

If no nxclient.cfg file is available, the NX Client Connection Wizard GUI is issued to allow the user to create either the client configuration file and the session file.

Please note that, since on Mac OS X  all applications are run from the root directory, the client would search for the nxclient.cfg file in the /.nx/config/ directory but it is forced to search in /usr/NX path to be compliant with the unix-based  O.S.