I use to have this problem, but after upgrading to Yosemite and changing how my monitors are connected, it’s keeping my configuration.
One question, when I was having this problem, the computer would boot to my left-hand monitor, it would show the boot screen with the spinning wheel, now the progress bar. While in the display preferences under Arrangements the titlebar was on my right-hand monitor. Now it working and both the boot monitor and the titlebar monitor are the right hand monitor. So the question, is your boot monitor the same as your titlebar monitor?
Yes, I’m grasping at straws, but sometimes it works.