Here is are some ideas that should help you find the 'missing' clients.
Go to one of the clients that have a green light. Open the SEP interface (You can double click on the shield icon) and click Help --> Troubleshooting.
There is an item called "Group:" This tells you what group the client is in. Also note the "Server" name, just to make sure they are not connected to some other server by mistake.
Go to that group on the SEPM server and look for the client(s). Be aware that the clients could be logged into the SEPM server using "User Mode". Mulitple clients can be logged in under one user if they are all using the same user name (The user name is the Windows login name). There is also a search function in the SEPM console that may help you find the computers.
If you need to check which domain the computer is in, you can open the Sylink.xml file on the client, located in the SEP install directory, and that will list the Domain ID. You can compare that number with the domain lists on the SEPM console.
I hope you can find those clients!