Suddenly noticed that as soon as a window now pops open the javascript VM starts going a little crazy, with links on the page behind the window unclickable and other functions seemingly randomly failing.
The behavior persists even when the window is dismissed. Behavior exhibited in at least FF and IE8
I'll dig into the code when I get a spare minute, just seeing if there are any clues to help me track it down.
Downgrading to previous release solves the problem.