I have a general question about Symantec Endpoint Manager (Sep 12), what would cause the Sep 12 server to say that machines are reporting in but when you go to the machine and they machine is up to date with definitions and then your force it to sync, the Sep 12 server still shows the machine not reporting any suggestions on how to fix this other than uninstalling and reinstalling it, I am thinkin its a server side issue, the System Admin thinks it's the client.

Green dot is not present?

Did you verify tcp port 8014 is open?

Exact version here?

See these:

Troubleshooting Client Communication with SEPM

Troubleshooting communication problems between the management server and the client

I agree with .Brian, check to see if the green dot is on the icon in the task tray.

Also you can open the client side by double clicking the icon, go to Help in upper right corner and select Troubleshooting.  Verify server its connecting to and last time it connected, as seen in screen shot.

Might be simple step but I would suggest you to try. Log off the SEPM . Restart the services of manager and database. If didn't fix. Simply delete the client in the manager by right click on client. It Will report back in few min depending on heart beat interval.

Open the client Help > Download Symantec Help Tool

See if that comes up with any issues it will also advise you of links to try and resolve the issue if it finds anything 

All of these are showing as reporting and I forced the synch but the reports we are getting from the Sep12 server are saying these machines arent reporting

Try this document first

Clients cannot send data back to Symantec Endpoint Protection Manager

http://www.symantec.com/docs/TECH105348

Post the sylink log

How to enable Sylink debugging for the Symantec Endpoint Protection 11.x and 12.1 client in the Windows Registry

Article:TECH104758

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Created: 2008-01-18

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Updated: 2014-09-29

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Article URL http://www.symantec.com/docs/TECH104758