Settings and configurations are not saved on Ubuntu 12.04 LTS

I recently installed 12.04 LTS. Whenever I rearrange the launcher icons they reset to their initial order after a reboot.

Also, although I can change the time and date settings, none of the changes I make reflect at all. The same happens when I try to add keyboard layouts.

They seem like different problems, but I think they are all related.

I think it's worth mentioning that I installed this 12.04 LTS version over an existing broken 13.10. A lot of things went wrong when I upgraded from 13.04 to 13.10, so I installed 12.04 and used the same username/password to maintain the files and folders in my home directory.