As SCOM is application as any other sometimes things go wrong. This was the case with one of our members (Jonathan) in system http://www.systemcentercentral.com forum. The issue is that a SCOM connector was not properly removed. I am sure you had this issue in 2007 version many times. There is even an KB article about this for 2007 version. For 2012 you can use PowerShell cmdlet. But in our case the cmdlet was failing to remove it. As there are no architectural changes to connectors in SCOM from 2007 to 2012 version I advised Jonathan to try the solution described by Kevin Holman here. He shows how t remove connector in 2007 with stored procedure in SQL. Jonathan tried the solution in his environment and this solved his issue. So it seems the stored procedures are still working in SCOM 2012 and can be used when needed.
I will advise to always try to remove the connector trough the official ways or contact Microsoft support. If you decide to use the stored procedure make sure you have a good backup before executing them.
This solution is provided ‘AS IS’ with no warranties.
All credits go to Kevin and to Jonathan who tested it.