yes, I am referring to the python window built into Arc. These scripts run fine outside of Arc, and even though you can call the same tools through the standard python window, I prefer to use Arc's "results window" to track the progress of the script and the various tools it is calling. Maybe this should be listed in the "ideas" section?
https://c.na1.visual.force.com/apex/ideaView?id=087300000008H7j&returnUrl=%2Fapex%2FideaList%3Fc%3D0...