Ubuntu :: Empathy Has No Menu Bar On Startup

I have Empathy set to start when I login, and when I turn off my computer, it is always still running. I also usually have Evolution, Liferea, and Rhythmbox running. All of these applications usually work fine the next day when I turn on my computer. However, for the last few days, Empathy has been starting without a menu bar. In one instance, Rhythmbox was also menubar-less. Now, Empathy is always without a menu bar. If I ever need the menu bar, I have to restart Empathy. Can anyone tell me why this is happening? I am unable to provide a terminal output since this application starts up with my computer. I have provided a screenshot of Empathy. I think I have a faint idea of why Empathy is without a menu bar. I read something somewhere about an XML file that contained the menu bar contents. I think that since I shut off my computer without closing these applications, that file has been corrupted. I have no idea why everything works fine once I restart Empathy, though. If you cannot answer this question, perhaps you could tell me if it is safe to shutdown Ubuntu with applications still running. In OS X, it will automatically tell your applications to quit safely, then turn of the computer. I hope Ubuntu doesn't just force quit any open applications. I am using Ubuntu 9.04 32 bit with the latest updates. I am using Empathy 2.26.1.