Mike,
I have ThinApp'd Wavereader 4.2 successfully after much troubleshooting, tested on XP and Win 7 (both 32/64).
Can you IM your personal email so that i can send you the entire ThinApp project folder (except bin folder) via dropbox?
All you need is just run the build.bat file that bundles your ThinApp license and creates the bin folder for you.