What user do python scripts run as in windows?

I've never used Python, but I would assume it runs as whatever user executes the script.

We've had issues removing files and directories on Windows, even if we had just copied them, if they were set to 'readonly'. shutil.rmtree() offers you sort of exception handlers to handle this situation. You call it and provide an exception handler like this:

import errno, os, stat, shutil

def handleRemoveReadonly(func, path, exc):
  excvalue = exc[1]
  if func in (os.rmdir, os.remove) and excvalue.errno == errno.EACCES:
      os.chmod(path, stat.S_IRWXU| stat.S_IRWXG| stat.S_IRWXO) # 0777
      func(path)
  else:
      raise

shutil.rmtree(filename, ignore_errors=False, onerror=handleRemoveReadonly)

You might want to try that.