Você esqueceu uma entrada "Monitor" na seção Tela.
Veja abaixo:
Section "Device"
Identifier "nvidia"
Driver "nouveau"
Option "Monitor-DVI-D-0" "samsung"
Option "Monitor-VGA-1" "acer"
EndSection
Section "Monitor"
Identifier "samsung"
Option "PreferredMode" "1280x1024_60.00"
EndSection
Section "Monitor"
Identifier "acer"
Option "PreferredMode" "1280x1024_60.00"
Option "RightOf" "samsung"
EndSection
Section "Screen"
Identifier "screen1"
Monitor "samsung"
DefaultDepth 24
SubSection "Display"
Depth 24
Virtual 2560 2048
EndSubSection
Device "nvidia"
EndSection
Section "ServerLayout"
Identifier "layout1"
Screen "screen1"
EndSection