I'll look into it. Since your description isn't exactly a recipe, I am going to have to do some testing to try to find the problem.
Sorry. I've never encountered (or at least noticed) it before so I'm not sure exactly what it takes to reproduce it. Probably I should have taken a bit more time to investigate before reporting it.
Perhaps the easiest work-around would be to not use the quick first shell tool. For the Au-Au parts of the fit, using the crystal structure for the pure metal is simple. For the Au-Ag, Ag-Au, and Au-Cl parts, it should be fairly simple to make a feff.inp file. For the mixed metal parts, try replacing the entire first shell with the other metal. For Au-Cl, try this: http://www.crystallography.net/cod/1510088.html
Thanks for the work around. Ian