I think that popup is just Win 7 being too sensitive about the anticipated results from the user's input if that input(installation) deviates in any way from Window's built-in programming parameters!

What I do when I get that message popup is go ahead and run the program, and if it runs as I expect, I just hit the "installed correctly" button and am not bothered about that installation again.

If it didn't install and runs as I expect, then I hit the "re-install using recommended" button and see if that fixes it. If It didn't install correctly  with Windows doing the installation, I manually install it again and usually it works on the reinstallation - I have never had to manually reinstall more than 1 time on my 32 bit Win 7 machine.

Hope that gives you some sense about how to deal with that bugaboo.