Hello,
Since you see the clients on all the VM machines properly installed and with green dots (which states they are reporting to the SEPM).
In this case, you may like to open the SEP client machine (which are not showing on SEPM), click on HELP, click on Troubleshooting and check the General Information.
It would show Server name, Group it is reporting to and Last connected status.
Could you upload us the screenshot of the same??
You can click on Update and check the SEPM again.
For further troubleshooting, check these Articles:
1) Symantec Endpoint Protection Manager 12.1 Communication Troubleshooting
http://www.symantec.com/docs/TECH160964
2) Troubleshooting communication problems between the management server and the client
http://www.symantec.com/docs/HOWTO55017
Hope that helps!!