I think we can close this although there should be some kind of warning that running an upgrade without an uninstall may not upgrade the files in some cases. However I can't really tell what those cases are. Since I deleted all the files and then did a repair with the new installer and still the old dll came back, I can't tell where it came from. Especially since all the files in the lib folder were the newer ones. Originally I thought maybe the dll was locked during the install, but moving the whole installation folder and creating a new one and then doing a repair still recovered the old dll. I was able to get some more information on this, because we actually checking the python binaries into our git repo to make it easy for other users to immediately startup and go without the need to install various binaries on their machine.