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:
(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".