when you open the settings page for a repository the settings pane is bellow the sidebar
What browser do you see this on? If you could also attach a screenshot, that would be great.
I just tried on Chrome and Firefox and it looks fine (I'll attach screenshots of the expected layout).
I Am on Google Chrome 26.0.1410.65
I'm also on Chrome 26.0.1410.65, btw.
This should be fixed now.