I’ve been playing around with my GSB files a lot - if I delete the whole directory and reinstall, or just uninstall and reinstall, the autopatcher doesn’t engage - instead I get error 41 again. I have the patch executables in my My Documents/My Games/Gratuitous Space Battles folder, but if I had deleted that as well I wouldn’t be able to patch. 
This is a disaster waiting to happen for people with a 1.00 installer.
Edit - Got a newer 1.03 installer - problem solved.