All these years, I always took a backup of my home folder. As part of that backup, the .config folder too was backed up. It was great joy to see that each time, the desktop settings, and other program settings automatically restored whenever the backup was restored. However, recently, I installed Ubuntu 12.04.2 LTS, Fedora 18 and then Xubuntu 13.04 only to find that in Xubuntu 13.04, somehow, something was not right.
The problem was the .config folder in my home directory. As the .config folder was restored each time after the Operating System was re-installed, I found that the settings from Gnome under Fedora 18, caused the misbehaviour when the .config was restored into the home directory in Xubuntu 13.04.
To overcome this issue, as part of the restore, I left out the restoration of the .config folder, and that resolved the problem. Remember, the .config folder will contain information of even stuff you do not need. So, do not restore this folder if you backed it up earlier from another distribution.