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Yes, its a little counter-intuitive to have to clear your focus when the point is to focus, but you have to make sure to do this before you try to use the link-backs, I have discovered. I have to make sure to clear the focus by invoking, "revert to default view" before attempting to use the links no matter what state OF is in.

Even when I have closed all the windows that utilized a focus this problem persists since opening a new window would reveal the focus is preserved. In fact, even if I invoke a different perspective (which you would think would clear the focus) the focus remains in the background and screws up the link back. If you see any focus in a window a link takes you to, this problem is present, I would think.

This is a known bug and omni ninjas have told me the are on it.

Now the good news, using perspectives does not seem to trigger this bug for me even when they involve a focus. So, if you just create a slew of perspectives to focus on those folders you commonly look at then you won't have problems with the linking. I normally do this anyway. So, I was very happy to see this bug did not effect perspectives.