Sorry for yet another long disappearance :( I've finally got a bit of free time, so I thought I'd come back to say hi.
Re: The Windows installer: Yes, it has that bug. It should be easily fixable. I'll look into it some more, but my initial idea would be to make something (windows mingw compatible script) to compile a list of all files in an ini format that would be included in the windows installer, and which will be removed during uninstall, leaving only empty folders. It might be able to be done completely with NSIS. I'll get back to you.
And welcome back Bradley. And thank you to Leo for you generous support. I wish I could help out myself, but right now, I have nothing to spare :( Give me 2-3 months, and I should be able to get some $$ to help out.