I tried to save X configuration to file but nothing changed, the same situation after reboot…
I tried to change VGA and DVI cables but it doesn’t help.
I had a similar issue with Fedora 20. I had my screens all set up in xorg.conf, just how I like them but new in Fedora 20 Gnome 3 had to be configured to agree with xorg.conf.
In Gnome 3 you enter Settings → Displays → Arrange Combined Displays and set things right there.
It took a few logins to get it right, but now I have no issues with that any more.
JBravo, thank you. I have solved this problem. I opened Settings Manager → Display and configured displays using it. After reboot there was no settings reset.