If all else fails, you may have to start fresh by using Knoxed Keis Files

Just seems as if there is some sort of permissions issue though

 

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.

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.

 

If you're not on a custom ROM then you should not be writing to "legacy" at all. You should just be writing to sdcard0 (or whatever you internal memory is called).

When you use "legacy" or "0" you're normally on a custom ROM and your sdcard0 should be "blank/empty". Like I said if you're not on a custom ROM then you should be writing to sdcard0. That may be your problem.

I have never had this issue myself so, my advice would be to do a clean flash and see if that works. (Assuming you have a custom recovery)

 

A backup normally doesn't create any issues since all it does is backup what you had set.

Have you tried changing the path to sdcard0 instead of legacy? If that doesn't work then, I would recommend you do a clean flash. Or you could try a different backup as well, to see if it was just that one backup that had an error.