Do you know if your python script is even being initiated when run as a scheduled task?
--According to the Task Scheduler Summary the runs are succeeding, however they finish in about 5 minutes (the model run by hand is approx 20 minutes to completion)
Are you using any SDE connections?
-- Yes, the initial connections are SDE, it then exports the data to a staging File GDB and finally to a Personal GDB for export to be incorporated to the outside program
Are you running the model itself on the 10.1 2008 R2 machine? Or did you run the model on another machine and just try to run it as a scheduled task on the 10.1 2008 R2 machine?