I have been experiencing exactly what is described here: http://arstechnica.com/civis/viewtopic.php?f=19&t=1225055
I've been having a strange issue lately where after waking from sleep, or logging in from the login screen using FUS, some of my previously open windows are shoved up to the top of the screen, partially under the menu bar, and much smaller than when the computer went to sleep/went to the FUS screen. If I try to resize the window, it snaps back to the smaller size. Likewise, if I'm able to grab a bit of the menu bar, I can drag the window down, but it will snap back right away. Quitting the offending apps (it's happened with Safari and Preview so far, but those are also the apps I'm most likely to leave open, so it may not be limited to them) usually lets me reopen the document/web page normally, although I've had to quit Preview twice a couple of times to fix the issue.
It doesn't always happen, but it first started happening a few weeks after I upgraded to Mavericks. I've taken a screenshot to show what it looks like, if that would help, but I'd need to figure out how to get it posted (I don't do any online sharing of pictures, so I'm out of the loop on hosting services.) This is on a 2008 iMac, FWIW.
I have a mid 2010 Mac Mini, single display. I have other symptoms like Transmission; if it is affected and it is active then it hangs when I try to quit it, and I have to force quit it. If it is idle and affected it quits normally. When Chrome is affected I can quit the app, relaunch and it will ask to restore, but the windows are normal width but about 1/4 of their previous height.
I see these log messages from all different apps on the Console after this behaviour happens:
12/30/2013 11:56:20.768 AM NotificationCenter: All available displays report that they are mirrors. This seems wrong. Please comment in <rdar://problem/14731307> if you see this log
12/30/2013 11:56:20.780 AM Dropbox: All available displays report that they are mirrors. This seems wrong. Please comment in <rdar://problem/14731307> if you see this log
Hoping others have seen this and may have a better grasp of what's going on.