I encountered a similar problem on the management Configure System page, while clicking on a checkbox for an optional block. I eventually tracked down the issue to a bug in the scrollIntoView function in hudson-behaviour.js (see here). This seems a generic enough function that I could imagine it causing problems in other places too.
The issue is that it's calculating the distance to move relative to the current scroll position, but it's obtaining the current scroll position from document.body.scrollTop which is always zero. It should be using document.documentElement.scrollTop (or possibly a combination of the two for backwards compatibility). Chrome used to support body.scrollTop, but that was a bug, and once that was fixed, anything that relied on the bug stopping working. You can read more about it in the Chromium issue tracker here and here.
This can be a difficult issue to reproduce, because sometimes it appears to work. But that's just because of another bug in the updateOptionalBlock function, which often returns a lot of NaN coordinates for the block's visible region. The result being that it just doesn't scroll at all (which is at least better that jumping to the bottom of the page).