The default WebSphere profile discovery is done by looking at registry entries.  Specifically, the WebSphere Management Packs check the registry of each user for an entry:

Software\IBM\WebSphere Application Server

 Unfortunately, this is a problem on Windows for the Network Deployment of WebSphere because the registry key is

Software\IBM\WebSphere Application Server Network Deployment

What to do?   Well, there are two options:

  1. Use the PowerShell-based discovery
  2. Create a new registry entry

For the later option, simply create a new registry key with the name Software\IBM\WebSphere Application Server. In it, duplicate the contents of the Network Deployment entry like the image below (click to expand).  The registry entry is a pointer to where the WebSphere MP discovery should look for the WebSphere installation.