Unless someone can find an authoring bug under Tools/msi, I don't think we can do anything about this. We rely on the built-in Windows support for adding and removing these variables, and if that's broken, we can't do anything with our current setup.

I really want to get us out of this addiction to cluttering up PATH with lots of different directories - it's bad for security/reliability/etc. of the system as a whole, and I don't like Python being the cause of issues here. But I haven't quite come up with the better design yet... 

Anyway, all that to say that I'm not in any rush to expand or seriously mess with the current PATH settings. If there's an authoring bug we can fix, great, but I don't think this one is on us in a way we can easily deal with.