For couple of months I am using Xubuntu 12.04 with multi-monitor configuration on one of my machines. I had experienced this issue since the beginning, but every week I found it more and more annoying.
The problem is, that on second screen (in my case the one on the right, but I checked different configurations) some windows disappears somewhere around middle of second screen. These windows are eg. terminals (all I checked - XTerm, gnome-temrinal and default xfce4-terminal), Notes app, Cairo-Dock. Apps that works (fortunately there is more of them) are all browsers, XChat, Skype, Calc, VirtualBox, Thunderbird or Ristretto (just the examples).
Do you have any ideas what is wrong and how to fix/workaround this problem? I can't find any solution or even similar problem on internet. I don't have too much experience with multi display configurations so I don't know if it is common issue or not.
I am using stock kernel 3.2.0 (now -33) and open source Radeon driver with Radeon X1250 integrated graphics card.
01:05.0 VGA compatible controller: Advanced Micro Devices [AMD] nee ATI RS690M [Radeon X1200 Series]