So This one comes from Microsoft TechNet forums http://social.technet.microsoft.com/Forums/en-US/virtualmachinemgrproscintegration/thread/dcf580e1-1366-4eed-967b-57b1062eba51/
Here you are the situation
You have PRO integration configured between SCOM 2007 R2 and VMM 2008 R2 SP1
PRO alert is being generated twice actually. There are 2 alerts in OM with the exact same time they were raised, the only difference is the alert ID.
a) Administration->Settings->DB grooming in OM console.
b) Run Set-VMMServer -OpsMgrServer "" (empty string) from VMM powershell, this will reset OM-VMM integration.