You can manually edit the oratab file and it should have an entry for each database in the form of

INSTANCE_NAME:ORACLE_HOME:STARTUP_FLAG

eg

TESTDB:/home/oracle/product/9.2.0.1:Y

Once you've added those entries try removeing the services.ora and snmp*.ora files and stopping and restarting the agent. Once you've done that check to see if the entries are recorded in the services.ora file.

Regards