@Marklar: I can't really think of anything. Any options that are set are set through BigWigs and would get saved as such. You could try to maybe delete your BigWigs.lua & .bak file in your savevariables, but it does sound pretty odd that they would get activated for one but not the other, especially when you can see them on the menu.
just to update this - i told you it would be something stupid. needed to enable bigwigs_plugins in the loading screen.