I'm using Fluxbox, but also I've installed few KDE, Gnome and XFCE apps - and this never be a problem before. Few weeks ago I've noticed weird dependency added for kde-plasma/kde-cli-tools and kde-plasma/systemsettings (I use the latest to configure some KDE apps), which was reported in bug 668988. As that bug was ignored I just let emerge install everything it wants, but it looks like now my notifications is broken.
When I start xfce4-notifyd-config it show warning "The notification service is not running. No notifications will be shown.", which is weird because /usr/lib64/xfce4/notifyd/xfce4-notifyd should be automatically started by dbus.
If I click "Show Preview" button and then look at process list I see this:
/usr/bin/dbus-daemon --fork --print-pid 5 --print-address 7 --session
\_ /usr/bin/dbus-daemon --fork --print-pid 5 --print-address 7 --session
\_ /usr/bin/plasma_waitforname org.freedesktop.Notifications
and later xfce4-notifyd-config show error "Error calling StartServiceByName for org.freedesktop.Notifications: Timeout was reached".
To me, all this feels like invalid dependency for some kde apps result in installing kde parts which are not compatible with non-kde desktop.
I had to remove these packages to remove kde-plasma/plasma-workspace and make notifications work:
emerge -av --depclean kde-plasma/plasma-workspace kde-plasma/systemsettings kde-plasma/kde-cli-tools kde-plasma/breeze kde-plasma/kde-gtk-config kde-plasma/kscreenlocker kde-plasma/kwin kde-plasma/plasma-integration