I see this happening too, but it's weird - we decide whether we can use ctags based on the scheme rather than the file extension, and .pyw is associated with Python so I'm not sure what's happening.
Using process monitor I can see that for some reason we're not forcing Python mode:
ctags --fields=+n -f - "C:\test\test.pyw"
I expect to see --language-force=Python in that line. In fact, I've just noticed this isn't happening for C++ either, so it looks like you just found a nice bug! Please report on the issue tracker and I'll get this fixed:
http://code.google.com/p/pnotepad/issues/entry