Crud, I just ran into this on gentoo after updating my system. Fortunately aticonfig --adapter=all -f --initial brought it back to life.
EDIT: I put a dummy dvi plug on the 2nd card while running these commands and booting the first time.
can you pull the dummy plug, restart cgminer and see if both cards work? it would be nice to know if it's only on set that it needs the dummy plug, or always.