Some folders won't open properly. Why?

Ever since upgrading to Mountain Lion (from Lion), there are a couple of folders that won't open properly. This isn't a huge deal, but it is annoying. I tried logging out and in again, repairing permissions, and verifying the disk, and none of them fixes this. Here is an example of the problem:
I open a new Finder window, and it starts out by showing my user folder as it should. Then I click the 'Downloads' folder to open it up. But what I then see, in the actual Finder window, is the user folder - just like before! - except the icons are a little bit farther apart (the toolbar says it's the Downloads folder). This also happens with a couple of the other folders, like Music and Pictures.
The folder itself is fine - I can open the Downloads folder from the Dock, for example. I just can't do it from an existing Finder window. Why not? How do I fix this?

Also: Setting the Finder to always open folders in a new window DID fix this, but I'd rather not do that if I can avoid it.

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[Resolve startup issues and perform disk maintenance with Disk Utility and fsck|http://docs.info.apple.com/article.html?artnum=106214]
[Using Disk Utility in Mac OS X 10.4.3 or later|http://docs.info.apple.com/article.html?artnum=302672]
[Disk Utility's Repair Disk Permissions|http://docs.info.apple.com/article.html?artnum=25751]
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