After almost year of success, SQL database failed to register in ArcGIS Server. Traced problem to secondary/failover server in cluster. Deleted secondary server from cluster and database now registers fine. Cannot add secondary machine back in. set up that secondary machine as own server and can add database fine. But cannot add to original setup. Can run ArcGIS Server manager of original on secondary machine, but cannot log onto secondary ArcGIS Server manager from anywhere else (i.e. http://ip.address.machine2:6080/arcgis/manager/site.html) fails. Can ping on network, log onto, etc. ipconfig /all returns virtually identical results for each machine. Ports look fine on each, no firewall. Can telnet to primary, but not secondary - possible troubleshoot aid?
My suspicion is that the folder permissions for the configuration store have changed somehow, which is a notorious occurrence with AGIS SVR. Are you using domain service accounts? Is the config store on SVR1 or a shared network location? Make sure the service account that is running SVR1 and 2 (should be same) has the correct permissions to the config store.