I use emacsclient (with Konsole tabs, if that matters). I usually have several emacsclient instances open in different tabs. When I start a clock and then get away long enough, Emacs will prompt me to resolve the idle time in different buffer that has the clock, usually in the first buffer that I get back to. But often I cannot type a response in this buffer, or in the original buffer's tab, so that I have to "killall emacsclient" and reopen all the files/emacsclient instances.
Anyone experience the same?