This is correct behavior when you save any configuration manually it gets stored under /apps/system folder. And when you have environment specific configuration checked in SVN it get saved under /apps/config-{run-mode}. When you manually go and update configuration you will notice that one copy gets created under /apps/system folder.
To answer for your question please make sure you have specific environment related config saved and committed in svn or else you can just have one copy under config.author folder for author all author environment.