Actually I went back through it and it should only be an issue if urxvtc is used; urxvt "should" always be standalone.  Unless they went and made it too smart for its own good, in which case there might be some option to make it behave the old way.  See http://www.haskell.org/haskellwiki/Xmonad/General_xmonad.hs_config_tips#Terminal_emulator_factories for details.  (I am assuming the problem is urxvt recognizes itself and uses the terminal factory to rub off a new window in the same process, which can't be given separate configuration information and can't be communicated with via xterm-style raw pty mode etc.)