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]}}]

Note: Replace `EvaluationNotebook[]` with `$FrontEndSession` to make the new setting effective for all notebooks in the current MMA session, and with `$FrontEnd` to make them apply to current and later sessions.

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

![enter image description here][1]

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  [1]: https://i.sstatic.net/afd2A.png