Is that the reason that you reinstalled everything, and that did not fix that issue? Or, it was NOT doing that before you reinstalled OS X?
This is not something I have ever heard of about Safari.
Open your System Preferences, then Accounts.
Click on the Login Items tab.
Do you see that SafariAlertPanel there?
if so, click on that to select it, then click the (-) at the bottom of that window to remove it. Unchecking the box does not remove it from that pane.