I think I finally figured this out. Apparently with the graphics layers,unlike most layers, you have to wait for the map to load before adding a new GraphicsLayer.
For example:
you can't just have
var NewGraphics
NewGraphics = new esri.layers.GraphicsLayer({});
map.addLayer(NewGraphics);
Instead you have to have
NewGraphics = new esri.layers.GraphicsLayer({});
dojo.connect(map, "onLoad", function() {
map.addLayer(NewGraphics);
});