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Ok, I think you have run into a bug that I accidentally introduced recently when trying to fix another big (apologies). I just stepped through the process myself again from scratch and found something awry with the PYTHONHOME variables throughout win_ros.
If you want to be sure, start again from scratch and follow the now slightly more verbose guidelines.
If you want to just skip to the chase and retry with a minimum of effort, on your linux box
> roscd win_ros; svn update
> roscd win_py2exe
> make clean; make
This will fix those exe's.
and you should be able to go. Thanks for identifying this.