I've had this problem with clip, joins, and selections when performing geoprocessing in the Python Command Window. Everything runs fine in ArcGIS 10.0, so this is definitely a 10.1 bug. It occurred before and after installing SP1 for Desktop Background Geoprocessing (64-bit). The error occurs on shapefiles and feature classes (GDB). I can run some commands referencing a layer and have it work fine, close ArcMap, open later to run the same commands and receive the error...Sometimes the error would appear for a different layer that didn't give me a problem before. Nothing change in the TOC or with the layers. FRUSTRATING...
My workaround...Every time I received the error I was referencing a grouped layer. Being grouped didn't cause the problem, as it occasionally worked with the same grouped layer, but errors only occurred on a grouped layers. If I moved the layer outside of the group the errors always went away. I've tried several ways to reference the layer (e.g. r'GROUP\lyr', 'GROUP\lyr', 'lyr) but could not find a solution.
As someone else mentioned, sometimes restarting ArcMap helps too.