What exactly happens with your kmix popup? I guess it's automatically started when you log in? But you do not only see the icon in the taskbar but also the main window, is that what you mean?
I had the problem described above. Then I found out that kmix got started twice when logging in. So I deleted my entry in ~/.kde/Autostart/ and it worked fine. This is the expected behaviour, when you start kmix a second time, the main window will pop up. In my case, kmix was once started because the session was restored, and once because of an entry in ~/.kde/Autostart/.
But I don't know if this is your problem or if your problem is something else, as I do not understand what you mean by "kmix panel popup".