It seems that IronPython 2.0.1 executes a script file about 3x slower than IronPython 1.x.
I'm not convinced that it isn't something I'm doing so I'm wondering if others have had a similar experience. 
I have a 200k python script that takes 5 seconds to execute from a file on IP 1.x and nearly 18 seconds in IP 2.0.1!
Does your timings include startup time?
IronPython 2.6 Beta has radical improvements to startup time and code compilation/execution. Suggest you try that release if you can.
Cheers,
Davy
IronPython 2.0 executes code slowly