Select Analysis of one feature

I have a python script that performs a select with a SQL expression against a feature class, thereby selecting a few features out of many. This all works fine unless there is only 1 feature in the selection. Then I get an error that says

ERROR 000372: Spatial Reference for output is invalid, Please update to allow output to become valid
Spatial index grid is too small
Failed to execute (Select).

The error is thrown but the output feature class is still created.

This worked fine in 10.0, but after the upgrade to ArcMap 10.1, I get this error. Any ideas?