If you have verified your configuration is actually correct, yet you still receive this error message:
Error in repository configuration: <repository id> not found
you may have encountered an error in the system.
This error only occurs if your configuration uses the Oracle DBMS. Fixed value for Oracle is set to 0, yet it is used in an integeter field. Therefore when the MDM API Factory class tries to check the configuration settings, its check for initial on the DBMS_TYPE field produces an error for the Oracle value - 0.
This problem occurs in MDM 5.5 SP4 up till Patch Level 2. OSS note 995252 contains details on the problems and the advance corrections that can be applied.