I have a Fedora system running with 3 monitors and recently did a yum update that did something to make the three monitors not all come back up properly when rebooted.
I have two monitors on DVI and one is VGA, I had to alter my ModeLine entry to get things back to normal, from:
Modeline “1680x1050_60.00” 147.14 1680 1784 1968 2256 1050 1051 1054 1087 -HSync +Vsync
to
ModeLine “1680×1050” 119.00 1680 1728 1760 1840 1050 1053 1059 1080
Option “PreferredMode” “1680×1050”
Now just as a note, the monitor DID come back if I just removed the ModeLine entry all together, but then the VGA screen was a low resolution. Hope this helps someone!