Version: (using KDE KDE 3.5.5) Installed from: Gentoo Packages I noticed this with gnucash, although it should affect other gtk/gnome apps. Reproduce: Try and close gnucash gnucash shows "Quit Gnucash?" modal dialog. Change focus with alt-tab or click, note that gnucash is no longer selectable with alt-tab. However, alt-tab and left mouse click on gnucash will focus it.
The dialog has _NET_WM_STATE_SKIP_TASKBAR set, which I consider a bug of Gnucash. The rest is a feature (bug #106818). You can explicitly configure KWin to override the setting for the application (Alt+F3 -> Special window/application settings -> Preferences, enable Skip taskbar, set to Force, set value to disabled). *** This bug has been marked as a duplicate of 106818 ***