Think it depends on whether you are cloning or extending the desktop. It can be a little difficult to setup. I would suggest, if you have not already, go to the Display Control Panel, Settings , select the 'Display' tab, then click on the Help button. Go to arrange multiple displays. It will tell you there how to assign displays, and retain settings under topic 'change the assignment.... This should then assign the resoluiton and settings you made when you reboot. I am not being glib, just making sure the basics are covered first. If you have done so already then I am uncertain why settings are not being retained. Perhaps others may assist you here.  Reply back with how things go.