Wow... I started at my current job about a year ago and we use Mac Minis as the main workstation for the users. Well as the users started doing more work we got them dual monitors and that is when I started noticing the first problem described. Everyday the same few people would come to me saying that their display settings would swap the main monitor, and sometimes it happened when they went to lunch.
I searched online and couldn't really find a sure-fire resolution. I did however, find that if I logged into the administrator account and swapped the monitors, then went into the Energy Saver settings and prevented the Mac from automatically sleeping when the display is off then it keeps the problem away long enough. I will usually have to repeat that process upon an update but I am just glad I found out why this was actually happening.
I searched online and couldn't really find a sure-fire resolution. I did however, find that if I logged into the administrator account and swapped the monitors, then went into the Energy Saver settings and prevented the Mac from automatically sleeping when the display is off then it keeps the problem away long enough. I will usually have to repeat that process upon an update but I am just glad I found out why this was actually happening.