I get a few these messages in my ~/.xsession-errors while running my xsession.
Sometimes applications do not get the input focus properly. The window is
active, but the application does not receive any keyboard input, mouse input
works. For example in a gnome-terminal the cursor does not become solid, in
xchat's input field I see no cursor and cannot type anything.

I haven't found a way to reproduce this (mis-)behavior yet. 

Some more (helpful I hope) information:
housetier@ganymede:~$ xfwm4 --version
        This is xfwm4 version 4.2.1 for Xfce 4.2.1
        built with GTK+-2.6.2, linked with GTK+-2.6.2.

I am using the debian packages from here:
deb     http://www.os-works.com/debian testing main
deb-src http://www.os-works.com/debian testing main
I use these with debian unstable/experimental