When recovering a Microsoft System Center 2012 Configuration Manager site that uses a remote instance of Microsoft SQL Server, if you change the SQL Server Service Broker (SSB) port during the recovery process, the recovery process finishes but the site remains in Maintenance Mode. Additionally, messages are stuck in the message queue and the SSB port is changed back to the original port that was used when the backup was created.
To work around this problem, do not change the SSB port during recovery. However, if you change the port during recovery and the site server is in Maintenance mode, change the SSB port back to the original port. This starts data replication working again and the site should exit Maintenance Mode. After the site replication links return to Active status, run Setup again and perform Site Maintenance to change the SSB port.
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.