Opening URL from OS X e-mail overwrites instead of opening new tab

Havent seen this before,and found no search hits on here.
I have my Safari preferences to "Automatically" open a new tab with a new link open. When I do this within Safari it works as expected (adds a tab to the right of all open tabs). I also have the "make a new tab the active window" option checked which works fine.
However when I click on a link in an e-mail (OS X Mail 6.2 (1499)), instead of the usual behavior it overwrites a random tab in safari and makes it active. Whatever was in that old tab (might be the third tab in an inactive window) is gone. Only way I can get it back is to reopen windows from last session.
Only change I have made recently is the 2.0 updater for mid-2012 Macbook Pros.
Any ideas? I have trashed the ~/Library/Preference

Replying to myself and bumping this up.
This behavior mysteriously stopped for a few weeks, so I forgot about it. Today, it started again. And it is not consistent: some links that I click in emails open a new window, as they are supposed to, but some links in emails pull up a random Safari window from my dock, and overwrite a random tab. Worse yet, the back button is grayed out, so I cannot even return to the page that was overwritten. So now I have to get back into the habit of reading an email, and if there is a link I want to click, I have to switch over to Safari, create a new window, then go back into mail and click the link. Frustrating!
Is Apple ever going to address this?

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