For the first part: I'm guessing that you're not running a stock fbpanel config, so the default config file didn't get upgraded as per normal. The menu file has been moved to /var/lib/fbpanel, since it's variable data, not config. If you correct your config to point to the new location of the menu file, all should be good.
For the second part: that is a result of my attempt to automatically reload fbpanel with new menu entries. Obviously killall -USR1 fbpanel is a slightly-too-broad brush to be waving around. I've implemented a totally different way of doing things for 4.1-2 -- I bit the bullet, learned a bit of GTK, and have put together an automatic config file watcher, so fbpanel will reload whenever any of it's config files changes. Yay! Look for a new version Real Soon Now. - Matt
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