I had the same problem. It took quite a long time to move all the icons back where they belonged after an iTunes restore and updating to 9.3.3.
I was using FolderCloser, InfiniDock and UpsideDown.
So here's a question. If I were to uninstall the above tweaks, make sure all the icons were in their correct positions; then do an iTunes backup, and then reinstall the tweaks -- would a subsequent restore keep the icons where they belong?