pdm_configure uses version control to help create the NX.env. One of the files that is important for this to work correctly is the client_nx.env file located in the site folder of the Service Desk install directory. pdm_configure will pull from the client_nx.env of the active background server and because of this, if the client_nx.env file is incorrect on the active background server, the NX.env file is not created correctly.