I am also experiencing this issue on my rooted Galaxy S2 with 4.1.2.
In addition to resetting my wallpaper, the backup also sets my default keyboard back from Swiftkey to the Samsung Keyboard.
In my case, it has been every time I run Backup - All User Apps and System Data.
By testing I have determined that if I do not backup Swiftkey then the default keyboard doesn't change.
In the case of the wallpaper issue, I Have not yet been able to work out which backup item is causing the problem.