have the same freaking issue, when i telinit 5 from konsole the only screen that will work is my plasma (connected, with VGA from DVI port on Nvidia Geforce 7800gt with adapter)
my main computer screen doesnt work, if i try to fix anything in the Administration - display my X.org crashes and i go back to konsole recovery.
If i unplugg the plasma my pc screen works like a dream!
Starting to hate Fedora Core 6.... was easier installing Fedora Core 5 on a laptop with "noname" chipset and ATI 9700 graphic
Seems like Xorg.conf is beeing changed every time i restart... to what i have connected. should it do that?
BTW be gentle, im a total Linux noob, only used linux for about 2 weeks now...