When a plugin such a Flash or Java becomes focused, Gecko gives the plugin complete control over the keyboard. You have to use the mouse to unfocus the plugin. For lack of a time machine to go back and throttle the individual who wrote this into the Mozilla platform, there happens to exist the following work-around in Conkeror. Bind a key in your window manager to run the following command:
conkeror -f unfocus
This command remotes the command unfocus to the active conkeror window. A message will appear in the minibuffer on success.
Further information: https://wiki.mozilla.org/Plugins:AdvancedKeyHandling