I have what seems to be the same bug. A few extra facts:
- Restarting Gnome Shell (Alt+F2, r) does not solve the problem
- I can give the focus to the phantom windows (with alt+tab or windows key), 
but they remain invisible. 
- The mouse cursor changes as I hover over different zones of the phantom 
windows. Eg., it turns to the resize cursor when over the (invisible) edges.
- When the phantom windows has focus, hitting alt+space brings the window menu. 
If I then select Minimize, and then switch to the phantom window using alt+tab, 
it reappears
- When the phantom windows reappear, the place they appear on screen does not 
match how they react to the mouse: mouse coordinates seem to be offset by a few 
hundred pixels vertically and horizontally. It also means they grab mouse 
events on zones of the screen that do not seem to belong to them.
- Extra weird: when attempting to resize a reappeared phantom window using its 
top or left borders (which is not easy as I have to blindly find the zone that 
gnome shell thinks is the window border), their apparent width or height do 
indeed change, but their position remain the same (ie. the border I am dragging 
doesn't move, but the opposite border does). Resizing using the bottom or right 
borders works as expected (except of course for the mismatch between mouse 
position and display position).
- When exiting reappeared phantom windows, their frame is still displayed, 
although it does not react to mouse events. It is drawn above all other 
windows. The windows do not appear in the alt+tab window list or in the exposé 
(windows key). Exiting from exposé mode, the frame come back and stay until I 
restar Gnome Shell.

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https://bugs.launchpad.net/bugs/1215798

Title:
  losing windows on Ubuntu 13.10

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