There used to be an arrow showing what section you are in. The earliest design post) shows it pretty clearly in this image under "Questions":
Another more recent example of the correct behavior can be found here.
Actually, this arrow is not completely gone. It's just a little too low now, as you can see on the main site (look carefully; it's a slightly different color than the background):
(Meta has the same problem, but you can't see the arrow because it's the same color as the background. I think that the arrow on main would look better if it matched the color of the background, but that's beside the point right now.)
The problem is in the CSS for this:
<li class="youarehere">…</li>
The padding for this element is 0 0 35px 0;. If you change the padding to 0 0 20px 0;, then the problem is fixed. I suspect that the new top bar height is responsible for messing things up.
