Did you create a custom shelf elsewhere? All my custom stuff sits in my shelf directory, which I've specified directly in the preferences. On my system, there is the "default" location for the shelf in the user documents directory, then one in the folder where I installed SP and one which I specified on my resources drive, which I have marked as default. All the 'normal / included' stuff sits in the folder off the install directory, but everything I have created or imported sits in my custom shelf.