I'm not in front of the pc now, but afair the problem was related to opening a new urxvt window FROM a running urxvt.
More details soon :)
urxvt defaults to using a client-server model for all terminals, IIRC (we have a warning about it in the xmonad documentation as well since it messes up ManageHooks). There's possibly some option to disable this and force an independent terminal.
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