When your in your ROM, your phone has a "emulated" section and its creates a "0" and a "legacy" section, as you probably know. For me, both the "0" and 'legacy" have the same exact files as my normal SD Card has (non-emulated section). I believe "0" and "legacy" are essentially the same thing, I think[/].
So, what exactly is your problem? Are your files missing? Can you go to the "0" section? (If you go up a level you should see "0" and "legacy" inside of the "emulated" folder)
Also, try using a different explorer such as, Root Explorer. If the issue still exists then it most likely is your ROM. If its possible, flash a newer version of your ROM. (i.e. CM11 Nighties) You can try doing a clean flash to see if the issues still exists. If it does, then its ROM.