the reason that can happen is that the saddle radius is .875". when you put a shim in the saddle, it reduces the width of the saddle by the thickness of the shim. when that happens, it tries to push the edges of the saddle apart when the rocker shaft bolts are tightended. in this case the stand/saddle just couldn't handle that much extra pressure. i can tell this will be a lot of fun to fix.
