Rather than using the system-config-video app, manually configure dual head through the Xorg config file. Everytime I have dealt with the gui's I haven't been able to get dual head to work at all. http://gentoo-wiki.com/HOWTO_Dual_Monitors this should help you out a greal deal, though you'll need to use lspci to determine the BusID for each card (it'll be different since you aren't doing dual head from one card).
Shoot me an email if you're still having trouble,
-Endy