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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.