When I had update my management console to 12.1.4104.4130 i have been getting an error on the symhelp. I cannot find a clear solution

Title: The Endpoint Protection Console is not using its configured ports
Product: Endpoint Protection Console

Status: Error

Symantec articles:

Which Communications Ports does Symantec Endpoint Protection use?
http://www.symantec.com/docs/TECH163787

Troubleshooting communication problems between the management server and the client
HOWTO80740

Details:
------------------------------------------------------------------------------------------------------------------
Error    Reporting Console (httpd.exe) is not using its  configured port {43} with a state of 8445.  The application   is using the port.
------------------------------------------------------------------------------------------------------------------
Ok    Tomcat Shutdown (SemSvc.exe) is using its configured port 8765 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Console Logon (SemSvc.exe) is using its configured port 9090 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Monitoring & Management (SemSvc.exe) is using its configured port 8446 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Management Console (SemSvc.exe) is using its configured port 8444 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Client Communication (httpd.exe) is using its configured port 8014 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Information    No application is using RADIUS Communication(httpd.exe)'s optional configured port 1812 with a state of 'Listen'. 
------------------------------------------------------------------------------------------------------------------
Information    No application is using AjaxSwing(SemSvc.exe)'s optional configured port 8045 with a state of 'Listen'. 
------------------------------------------------------------------------------------------------------------------

It looks like during your management configuration wizard your port got changed from 443 to 43. Re-run the configuration wizard and change the reporting console to 443.

port 43 is incorrect, needs to be 443

It still didn't work I get this now.

Title: The Endpoint Protection Console is not using its configured ports
Product: Endpoint Protection Console

Status: Error

Symantec articles:

Which Communications Ports does Symantec Endpoint Protection use?
http://www.symantec.com/docs/TECH163787

Troubleshooting communication problems between the management server and the client
HOWTO80740

Details:
------------------------------------------------------------------------------------------------------------------
Error    No application is using Reporting Console(httpd.exe)'s  configured port 8445 with a state of 'Listen'. 
------------------------------------------------------------------------------------------------------------------
Ok    Tomcat Shutdown (SemSvc.exe) is using its configured port 8765 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Console Logon (SemSvc.exe) is using its configured port 9090 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Monitoring & Management (SemSvc.exe) is using its configured port 8446 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Remote Management Console (SemSvc.exe) is using its configured port 8444 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Ok    Client Communication (httpd.exe) is using its configured port 8014 with a state of 'Listen'.
------------------------------------------------------------------------------------------------------------------
Information    No application is using RADIUS Communication(httpd.exe)'s optional configured port 1812 with a state of 'Listen'. 
------------------------------------------------------------------------------------------------------------------
Information    No application is using AjaxSwing(SemSvc.exe)'s optional configured port 8045 with a state of 'Listen'. 
------------------------------------------------------------------------------------------------------------------

We're going to need more information then.  Under %Symantec install directory%\Tomcat\Logs there is a file called scm-server-0.log. We need to know what errors are appearing in there. And what symptoms that you are having.

whats the result of Netstat -ano

Do you see 8443 , listening? if Yes the you can ignore the error message.

No 8443 is not listening.

2014-06-05 10:20:44.578 THREAD 12 SEVERE: FIPS mode configuration is false

Then its complaining the right thing. 

Still getting a port error 

Title: System does not meet the requirements for Symantec Endpoint Protection Manager 12.1
Product: Endpoint Protection Console

Status: Error
Overview: Does your computer meet the system requirements for Symantec Endpoint Protection Manager 12.1?

Symantec articles:

Release Notes and System Requirements for all versions of Symantec Endpoint Protection and Symantec Network Access Control
http://www.symantec.com/docs/TECH163829

Details:
------------------------------------------------------------------------------------------------------------------
Error    Title: One or more default ports for Symantec Endpoint Protection Manager are not free
    Symantec articles:
    Which communications ports does Symantec Endpoint Protection use?
    http://www.symantec.com/business/support/index?page=content&id=TECH163787
    Error    The process tomcat6 (Process ID 6992) is listening on the Symantec Endpoint Protection Manager default port 8443
    Information    The Symantec Endpoint Protection Manager process httpd (Process ID 11672) is listening on its default port 8014
    Information    The Symantec Endpoint Protection Manager process semsvc (Process ID 5520) is listening on its default port 9090
    Information    The Symantec Endpoint Protection Manager process dbsrv12 (Process ID 13572) is listening on its default port 2638
    Information    The Symantec Endpoint Protection Manager process semsvc (Process ID 5520) is listening on its default port 8765
------------------------------------------------------------------------------------------------------------------
Ok    Your operating system version (Windows 2008 R2 Server Standard (full installation) Service Pack 1 64-bit) is supported.
------------------------------------------------------------------------------------------------------------------
Ok    Available disk space (197.11 GB) on the system drive meets the recommended 100.00 GB.
------------------------------------------------------------------------------------------------------------------
Ok    Total RAM (32.00 GB) meets the recommended 4.00 GB.
------------------------------------------------------------------------------------------------------------------
Ok    At least one of your displays meets the recommended display resolution.
------------------------------------------------------------------------------------------------------------------
Ok    Microsoft Internet Explorer version 9 is installed.
------------------------------------------------------------------------------------------------------------------
Ok    Title: The current user is logged into a domain
    Symantec articles:
    Is the local security setting 'Sharing and security model for local accounts' set to Guest Only?
    http://www.symantec.com/docs/TECH106144
    Ok    The user is logged into a domain: suthprod
    Ok    Simple File Sharing is not enabled
------------------------------------------------------------------------------------------------------------------
Ok    Title: The current user has local administrator rights
    Symantec articles:
    Does the current user have local administrator rights?
    http://www.symantec.com/docs/TECH91646
    Ok    The current user is a member of BUILTIN\Administrators
------------------------------------------------------------------------------------------------------------------
Ok    Title: User Account Control (UAC) is not present or not enabled
    Symantec articles:
    Is User Account Control enabled on the client?
    http://www.symantec.com/docs/TECH91902
    Ok    UAC is not enabled
------------------------------------------------------------------------------------------------------------------
Ok    Title: The Windows Installer service is enabled
    Symantec articles:
    Is the Windows Installer service disabled?
    TECH92579
------------------------------------------------------------------------------------------------------------------
Ok    Title: SQL Server or client is installed
    Ok    Microsoft SQL Server 2008 is installed.
    Ok    Microsoft SQL Server Native Client 10 is installed.
------------------------------------------------------------------------------------------------------------------
Information    Endpoint Protection Console 12.1.4104.4130 is already installed.
------------------------------------------------------------------------------------------------------------------

I ran the update.bat and completed the wizard and still not configured correctly. From the looks of it doesn't meet requirement for the console because of the process tomcat6 (Process ID 6992) is listening on the Symantec Endpoint Protection Manager default port 8443. Ever since i had update the Symantec error I have been getting errors.

That would seem to suggest you have another tomcat based application running on this server as well.  Is this possible?

If that is the case, I'd recommend removing it and repairing the SEPM (as it goes against Symantec recommendations to install the SEPM on a machine with any other tomcat installation running).

If this is not the case, and symhelp is somehow erroneously classifying the semsvc process as tomcat6 instead, then you might need to log a support case or perform a DR (full uninstall/reinstall).

Well i have nova backup management console and a NAS running on the server can that be the case.

definetly a port conflict, stop that tomcat service and run the management server config wizard.. if all is well then you need to replace the port / app

follow this

How to change server port 8443 of the Symantec Endpoint Protection Manager

http://www.symantec.com/business/support/index?page=content&id=HOWTO59234

I'm not familiar with Nova backup, nor whatever NAS you have, so I'm afraid it's up to you to investigate if that is what is causing the port conflict.

I'd personally recommend sticking SEPM on a dedicated machine if at all possible though.