Adam,
 
Basically, once py2exe is used, Python does not see/use the Lib folder

that is the expected behavious. py2exe goes through great pains to load modules from the library.zip or, in case of single-file-distribution, from the library file integrated in the single file.

That behaviour can be changed. You have to add your "own" importer (which should be nothing more then the standard file-system-importer) to the chain of importers

I do not know of a one click solution. Read up on importers:

http://docs.python.org/library/imputil.html
http://docs.python.org/release/2.3.5/whatsnew/section-pep302.html
http://www.doughellmann.com/PyMOTW/sys/imports.html

(The "import chain" has to be modified within your application when py2exed.)

It is definitely possible to solve your challenge; to read more background you may use the google words "python custom importer". 

Best wishes

Harald

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