I don't know how to use IME with litestep (I don't think it is supported) so I'm forced to use the floating toobar version of it.
If your IME bar was part of the taskbar in explorer, then you're going to have to go back to explorer (the shell not file manager) and change the settings to "show the language bar on the desktop".
Sometimes when you click on something litestep related, eg a popup or the desktop, it disappears but reappears when you click on a different program.