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:
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.