The problem is that the desktop shell does not properly attach to the signals of seats that get added after the shell is initialized. This results in xdg_surface.[de]activate events not being sent to clients when running under the RDP or Wayland backends.
This is fixed by the following patch: http://lists.freedesktop.org/archives/wayland-devel/2014-April/014356.html
commit 024177cecb5bfad228804656e17ac02ac6fd96bf Author: Jason Ekstrand <jason@jlekstrand.net> Date: Mon Apr 21 19:42:58 2014 -0500 desktop-shell: Properly handle seat hotplugging Previously, desktop-shell would only create its internal shell_seat object for each seat available when the desktop-shell module is loaded. This is a problem any time seats are created dynamically. In particular, the Wayland and RDP backends create seats on an as-needed basis and they weren't getting picked up proprely by desktop-shell. Fixes: https://bugs.freedesktop.org/show_bug.cgi?id=77649
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