Does the main window of the application not close when the popup dialog appears? On my system, the main window closes before the popup (though the entire process takes about a second in total).
From your log, it looks like it's partially shutting down, but not closing completely (some threads are exiting, but not all). The last few lines of my debug.log after shutting down Bitcoin-Qt look like this:
2014-10-27 02:24:59 Requesting shutdown
2014-10-27 02:24:59 Running Shutdown in thread
2014-10-27 02:24:59 opencon thread interrupt
2014-10-27 02:24:59 addcon thread interrupt
2014-10-27 02:24:59 dumpaddr thread stop
2014-10-27 02:24:59 msghand thread interrupt
2014-10-27 02:24:59 net thread interrupt
2014-10-27 02:24:59 Shutdown : In progress...
2014-10-27 02:24:59 RPCAcceptHandler: Error: The I/O operation has been aborted because of either a thread exit or an application request
2014-10-27 02:25:00 StopNode()
2014-10-27 02:25:03 Shutdown : done
2014-10-27 02:25:03 Shutdown finished
2014-10-27 02:25:03 Shutdown result: 1
2014-10-27 02:25:03 Stopping thread
2014-10-27 02:25:03 Stopped thread
My best guess is that something got corrupted and is preventing it from shutting down cleanly. If you haven't tried it yet, reinstalling the client will probably fix it, otherwise deleting everything it the datadir except your wallet.dat and the "blocks" directory might help (if you have a custom config file, check to make sure it's correct rather than deleting it). You may need to start Bitcoin-Qt with the "-reindex" parameter to rebuild the chainstate afterward, though it will likely do so automatically (it won't need to redownload anything if you leave the "blocks" folder there, but it may take several hours to finish processing the blockchain).