I have one server that has Content Manager and ATC components installed. When the server is booted, the Content Manager service does not start but all of the others do. There is a message in the log that the Content Store, which is on a separate server, cannot be reached. However, if I test the Content Store connection, it tests fine and if I stop and start the Cognos services, it connects fine. It seems that the Content Manager service is trying to read the Content Store but something hasn't started which allows it to do that. However, after all of the Cognos services have started, whatever is needed to read the Content Store is now running. Hopefully I have made this easy to understand. Has this happened to anyone else?
The Content Store is a schema/database . Have you checked if the service for that schema has started before the Content Manager service attempts to start?
The first place to check is the server log file. This will show what errors you are getting (sometimes cryptic) but it may tell you at what point it fails.