I don't think rooting had to do with it directly.
Android moved the virtual sdcard folder down one level and probably some program, possibly recovery itself, didn't account for that change and things are in a confused state. Probably your virtual sdcard is one level higher than Android expects. Possibly it happened on a restore.
Disclaimer: No touchscreens
were harmed nor injured during the creation of this post. GPS
units were all treated ethically and humanely.
Signed: People against misbehaving Nexus 7 2013s