Many people had this problem, but normally some dba find wrong way to solve this issue recreating the repo.
The EM has simple config, and you must sure that the parameters are correct. Some times the problem occurs because directory or system variable are incorrect.
Verify
SID/Service_name and ORACLE_UNQNAME variables that must correspond with directories name:
$ORACLE_HOME/oc4j/j2ee/OC4J_DBConsole_host_databaseName
The 'emct start dbconsole' command get errors when some parameters are wrong and "DBAs" recreate repo every time that get errors. It´s a poor resolution!
When you get Enterprise Manager oc4j configuration issue check the system vars and directorires and solve the problem as true DBA