Ringtones directory won't update in settings I removed some of the stock ringtones (from my ROM) that I didn't want from /system/media/audio/ringtones and added some new ones that I got from the xda forums via my SD card and RootExplorer.

When I open the Sound/Default Ringtone menus in settings, some of the old ringtones are listed and new ones are listed as well, none of them play. The only ones that do are the few that I left in /system/media/audio/ringtones and a few stored on my SD card.

How can I fix this issue so that my phone recognises that all files are in their proper directories?
To update the ring tone directory, the media scanner has to run. Usually restarting the phone will do this, but if media scanner is not checking that directory when the device starts you can try to create a file in the sdcard ringtone directory with an app that triggers media scanner. I think Astro File Manager will trigger it. 

If that doesn't work, you could try clearing the cache (I assume root since you are using root explorer and deleting system ringtones), the system may be caching that information and thinks they are still there.