You may need to add that map as two separate dynamic layers, and specify the relevant visibleLayers for each dynamic layer.
- create a dynamic layer for the polygon (eg, visibleLayers = [2]) and set its opacity to 0.6
- create a dynamic layer for the points, lines and annotations (eg, visibleLayers = [0,1,3])
Then how does arcgis.com does it, when you open a dynamic map service in arcgis.com. It shows a layerlist on the left. That means it loads each layer as a synamic layer spaerately?
I think ArcGIS.com creates a single dynamicLayer, which contains multiple layerIds. Each layerId is shown as an item in the layer list.
What happens if you add your layer to ArcGIS.com - does the polygon correctly show with 60% transparency?