I can't reproduce this here with my 3 monitor system...
mutter via gnome-shell writes out the monitors.xml, in exactly the same format as g-s-d and it will get read back in at startup unless there is some sort of race condition messing things up. (gdm/Greeter configs are currently unsupported, but I have a patch for that will atleast get uploaded to utopic at some point.)
I can't reproduce this here with my 3 monitor system...
mutter via gnome-shell writes out the monitors.xml, in exactly the same format as g-s-d and it will get read back in at startup unless there is some sort of race condition messing things up. (gdm/Greeter configs are currently unsupported, but I have a patch for that will atleast get uploaded to utopic at some point.)