I'm using LR 4.3 on an iMac (2012) running Mtn Lion 10.8.2 and am experiencing a strange phenomena (bug?) I have two monitors and normally run the second monitor option in LR. Whether or not the "secondary window" option is on or not, every time I leave LR and come back to it there is an extra and smaller secondary window sitting on top of my main window. The only way to get rid of it is to press the icon/button for the secondary window. If I already had the secondary window open then there are a total of three LR windows. Otherwise the button turns on the real secondary window (on my second monitor) and the little extra one disappears. The extra smaller secondary window is a mirror (though much smaller) of the real secondary window running on my second monitor. This is REALLY annoying as it happens every single time I leave LR, even for a few seconds to go to any other program such as PS, Mail, Safari, etc. Once the third window issue starts, it is consistent. However the issue itself only happens intermittently.
In the little secondary monitor pop-up menu, check Show Second Monitor Preview is turned off.
If that doesn't do the trick, I'd reset the preferences http://members.lightroomqueen.com/index.php?/Knowledgebase/Article/Vie w/1148/198/how-do-i-delete-the-lightroom-preferences-file