Contacted esri support. There is a bug, NIM088894, which states that the token generator from http://<server>.<domain>.com/webadaptor/tokens does not work unless the Web Adapter name is 'arcgis'. I tried to genericize my URLs but in actuality my Web Adapter was not named "arcgis".Unistalling and reinstalling the Web Adapter using the name "arcgis" (lower case) fixed the problem. The original token service now works.