I have always used Ubuntu Tweak to set my default user folders (download, pictures, documents etc.)
Since I upgraded to Ubuntu 14.04, the changes that I make to my user folders are not persistent, i.e., I have to reassign them using Ubuntu Tweak on every boot.
If it's helpful, two of the folders (music & video, if it matters), which are assigned to an external USB hard drve, do actually persist. The rest are on the internal HD and do not.
If anybody has experienced this issue or has any guidance I'd be grateful. I have hunted for answers to this question and found very little useful information.