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Layers of an ArcMap document may contain transparency. Layer transparency can be set within the layer properties or by using the effects toolbar. If you change the transparency value of a layer in a map document that you are currently using in an ArcMap Service and you refresh the ArcMap Service, the service should honor the change in transparency.
In some cases the transparency change is not honored.
ArcMap Server will not respond to changes made to layer transparency if the transparency was initially set in the display tab of the layer properties. Only the initial transparency value will be respected by ArcMap Server. However, any change made after saving and serving the map document either using the effects or setting the new value within the display tab of the layer properties will not be respected.
When changing a layer's transparency setting after creating an ArcMap Service, use the effects toolbar to initially set and then to make any changes to any layers with transparency.