I have done some checks and I think I know the answer.
I think most people are using this command to truncate the layer (delete all records).
In 10.0 the GP would just delete row by row keeping the spatial index.
In 10.1 the GP delete the spatial index, delete the row and rebuild the index. If you delete all records it is much faster.
If you delete just a few records it takes time to rebuild the index for the remaining records.
That is what I found checking trace file of enterprise geodatabase, I this it is the same for FGDB.