But how did you ran logstash when running in the CLI? You didn't say.
Assuming that you installed Logstash using the RPM, when you run it as a Service it will run as the logstash user, if you run it in the command line as root or using sudo, it will run as the root user, this can give you issues since Logstash create some files and if you try to run it as a service after the user may not have all the permissions it needs.
Do you have the file /usr/share/logstash/.logstash_jdbc_last_run ?