I have had problems like this and it's due to file/folder permissions and/or UAC, though I'm not quite sure which. Are you using Vista?
I started to go through files and folders to change their permissions but found this didn't solve the problem. I noted that I recently went from UAC being completely off - to UAC in "silent mode". I switched it off completely, ran SyncBack again and it seemed to work absolutely fine again. I'm not sure what caused the problem since I only have one user account on my PC anyway.