same situation here... No app called Shell to deny, and it usually happens when the phone freezes for a minute or two. I updated the su binary in superuser from 3.1 to 3.1.1 today and it made no difference. Still locks up once every few hours. Haven't found a conclusive solution yet...
Oh, and the phone is a Samsung Galaxy s3 rooted stock.
ETA. Forgot to mention, mine seems to be triggered by one particular folder in my gallery, specifically the folder that holds all the camera photos. Any of the folders in the gallery work fine, but the camera folder seems to be the sticker for some strange reason...