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Self-signed certificates are normally not recognised by the JVM. If the JVM needs to make any SSL connections that use self-signed certificates, you need to add those certs to the key store of the JVM that's making the connection (in this case the JVM used by the installer).
You will also need to add the cert to an JVM that will be publishing to this server, and possibly to the JVM of the server itself.
The browser is smart enough to ask you whether you want to accept the certificate, but the JVM has no way of asking you.
I hope this helps.