Thank you for noticing my sending mistake, Takanori.

This....

import os, __main__, wx

os.environ['PYMOL_PATH'] = "C:\Python27\PyMOL"

pyMolX=300
pyMolY=500
__main__.pymol_argv = [ 'pymol', "-qxX",pyMolX,"-Y",pyMolY] # Quiet, no ext GUI, pos(pyMolX,pyMolY)
import pymol, pymol.cmd
pymol.finish_launching()

pymol.cmd.load("water.pdb")

...fixes the problem with initial values, but I have yet to find a way to deal with freezing after "cmd.window()" calls on Windows.

I noticed that manually inputting "cmd.window('position',x=100,y=200)" in the external GUI or internal command line does not cause freezing. Is there a way to pass a string to the PyMOL interpreter externally with python?