I have that problem with my multi-screen setup but Desktop_OK can help, it saves the locations and helps you restores them, works about 80% of the time.
I have a dual view DVI Kvm that throws the occasional fit, probably because it switches two of three monitors across two workstations, combined with DisplayFusion and Mouse without borders, I think I'm pushing my luck!
I'm going to have duplicate icons anyway, because of the different machines, so I've come to terms with the chaos, and playing hunt the icon is always fun!