I encountered this replica is inconsistent error for protection status of SharePoint Farm Configuration Database under Protection tab inside DPM 2007 Administrator Console. The suggestion given by DPM admin console to solve the error is by performing consistency check on the farm configuration database. However after running the consistency check for several times, it didn't fix the error and consequently all protection activities, like recovery point creation for the SharePoint farm also failed.
After some troubleshooting, I found out that the root cause of this issue was due to the addition of a new content database to store a new site collection in the SharePoint farm. This made the replica of the data source (content databases) are inconsistent with the data source (content databases) on the protected farm.
To solve this issue, I need to modify the protection group, containing the error, by re-running the wizard (right click the protection group under Protection tab and choose Modify protection group). Then just clicked the Next button and finally the Update Group button to complete the process.
Tips: In the first screen of the Modify protection group wizard (Select Group Members), you have to expand the SharePoint server node under Available members until its farm configuration database node is displayed before clicking the Next button. Without doing this, the Modify protection group wizard will not be able to fix the inconsistent replica issue for the farm configuration database. This is the most tricky part.