What about this application modal popup window appearing behind the DOS window? (See attached) That popup window may only need to have a system style flag to push it to the top of the window z-order stack.

What causes that popup to appear? Is it Python source code or compiled C code built into python.exe?

There is a MS-Windows win32 function called SetForegroundWindow() that may be the issue if it's not Python source code.
Maybe this URL might shed some light on the popup issue?

http://stackoverflow.com/questions/3772233/win32-setforegroundwindow-unreliable

I am grasping for straws here.

Perhaps the python.exe app crashes in the cmd.exe window because of attempts to do something with the cmd.exe window while the app modal popup windows is behind it? 

As per my previous post is seems mhammond has a solution for his pythonwin package causing python.exe-help()-modules to crash. (If that's the case) it still doesn't address "other" packages having the same ability to crash python.exe, IDLE and other interactive interpreters thru help()-modules.