Similar to this post No ibus icon in Kubuntu, I have trouble with the ibus icon in Ubuntu 12.04. Each time an update is installed, the language selector for Japanese disappears from the top panel. I need to uninstall and install Japanese again, then reboot, to make the symbol appear again. In this thread No iBus icon in Kubuntu 12.04 the suggestion was to install the Japanese Version of Ubuntu, but is it really true that one has to stick to a special version of Ubuntu to get this problem solved? If so, how can I transfer the settings easily from the current version to the Japanese one?
If you are using vanilla Ubuntu, maybe you can try this command when the ibus indicator disappears.
If you are using Kubuntu, make sure that you have