To prevent your second invocation of `SetOptions` from resetting the value of sub-option `"SymbolContextStyles"`, you need to set both `"System"` and `"Global"` sub-sub-option values at once:

    SetOptions[EvaluationNotebook[],   
        "AutoStyleOptions" -> {"SymbolContextStyles" -> 
                                 {"System`" -> RGBColor[211./255, 54./255, 130./255], 
                                   "Global`" -> RGBColor[181./255, 137./255, 0./255]}}]

This setting works as expected on my Windows 8 (64bit) system with Version 9.0.1.0.