I was noticing the same thing. I am rooted, and I was backing up via Clockworkmod, and once it completed, I couldn't find the backup in the normal SDcard location. It is no longer storing on the SD card ,but in two places, data/media/clockworkmod and mnt/shell/emulated/clockworkmod.
Couldn't access the location as I wanted to copy it offline if needed. I could only access it via Root Explorer. I deleted it as it was taking up too much space. Once I deleted from one location, it deleted from the emulated location.
I may try something other than Clockworkmod which has been buggy lately.