I have both Gnome and KDE installed on my system. In Gnome I am able to split my desktop across my two monitors. When I go into KDE the monitors are cloned, and when I try to go into the multi-monitor settings, it says that its not able to do it.
i successfully used /usr/bin/krandrtray from the package "kdebase-workspace" to manually set the position of the second monitor. . i wonder if the program you used from within KDE was actually the one for gnome? i seem to recall that was my problem at first.
My box is CentOS6.4 gnome and KDE.