I can't explain where the Registry settings went - but it should explain why you see "x:\Microsoft Visual Studio\VC98\lib" ...
You must have environment variables PATH, LIB, INCLUDE pointing at some MSVC installation. You will see these values when there are no settings in the Registry (=use defaults =use environment).
If you use the "New folder" button, to the right of the Type combo, in Tools -> Options -> Folders, and add a new folder, the settings will differ from the defaults (in the environment), and the value will be saved to the Registry...
Pelle