I don't have a white dot next to open applications on my doc

I just got a new logic board for my computer. Now, when I have applications open there is no white dot next to their icon in my dock. The only exceptions are applications that are open on login (Finder, etc.)
Any ideas?

Actually, it's worse than that! When I use Command-Tab, I only see the applications that started on startup, nothing else!

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Hi,
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Setup Assistant can only be used at first install - otherwise you have to reinstall to use it.
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I don't have a white dot next to open applications on my doc

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