When Google decided to have one partition on Android rather than system and storage (remember when we ran out of space to install apps and want to move them to them to \sdcard) and with JellyBean to support multi-user capabilities this will be the norm... for each user, there will be a sequentially numbered folder in /data/media (/data/media/0, /data/media/2)...etc.
For each user /sdcard & /storage/sdcard0 will be linked to that users /data/media/"folder number".
User 1, /sdcard = /storage/sdcard0 = /data/media/0
User 2, /sdcard = /storage/sdcard0 = /data/media/1,
These are emulated storage points... /data/media/0 = /storage/emulated/0, /data/media/1 = /storage/emulated/1
Without root access, each user will just see /sdcard/ and will not be able to access the other emulated storage points, therefore it becomes a bit confusing to the rooted user.
In the recovery mode, however, /sdcard is mapped to /data/media which is why you need to navigate to the "0" folder to see your files
Please note that I have not loaded a custom ROM, so I cannot say that the file structure holds true as I have presented it.