@InfinityBeing I think that the problem is that ES shows all the directories that contain files with the extensions listed in es_systems.cfg.
For example my port system is configured to only show sh and SH extensions. I have several subdirectories in /home/pi/RetroPie/roms/ports, but since none of them contains *.sh or *.SH files they do not show up. If I create a directory in /home/pi/RetroPie/roms/portsand copy an .shfile into it, the directory will show in ES.
I guess that your CaveStory subdirectory contains a file with an extension listed in the port section of your es_systems.cfg. To have the directory to not show up in ES I suggest you move it to another location, and update the Cave Story shell script to point to this location.
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