I submitted this issue to Apple as bug # 19327689, and it was almost-immediately closed as a duplicate of 18525321. Unfortunately the latter bug is still open, and is not listed on Open Radar.
This is a known issue when an external monitor is set as the primary monitor. If you leave the primary monitor set as the laptop screen you shouldn't have this issue. Apple is aware of the problem and they are working it.
Which OS are you running? We ran into it in Mavericks, but I believe was resolved in Yosemite iirc.
We have the same issue with Mavericks and Yosemite. I found that if you remove the "com.apple.windowserver.plist" file from /Library/Preferences directory that will "reset" the display startup options. I created a policy that runs a the follow command and stuck it in Self Service.
rm -f /Library/Preferences/com.apple.windowserver.plist
Hope this helps!
If the user cannot login this does not help obviously. I assume this would require some education, i.e. letting the user know to unplug the secondary display and then have them run the self service script after login.
You are correct. Once they know to unplug the monitor and then to check Self Service. Most of our Mac users are in one department, so the word got around quickly.