I activated the new config framework and tests confirm it works in Konqueror, Firefox 2.0.0.4 Linux, IE7 Windows, and Safari Windows. If you refresh your browser cache you'll see a new config item in the ''misc'' tab of [[Special:Preferences]], you can toggle and save, and see how you can make the "Subpages" link in the toolbox vanish. If this is confirmed to be working (really make sure your caches are cleared and wait about half an hour before reporting a bug, I had similar problems as some people on the list today) we can add more config options and make more tools configurable.
Right now the options are stored in cookies, but you can also set options in your monobook.js if you want them more permanent.