I just recently updated to 29.0.1795.54644 and when i go to File - New window, File - New private window or have a login popup for commenting on open id enabled sites there's always a few (3 to 5) second delay before it shows up. The whole browser doesn't respond until the new window pops up. Is this happening to anyone else?

Yeah, same problem here. Just upgraded to the latest flash version, 15.0.0.152