FYI.
Tested the below scenarios in the ArcGIS Online and Portal
Just tested two cases in the webmap.
1. Adding entire map service to the webmap. Eg: http://skksfla/sdfkalsdf/mapserver
In this case, it will add a group layer with all the layers in the map service...enabled and configured popup... popup window NOT WORKING in this case..
2. Adding one layer from the map service to the webmap Eg: http://skksfla/sdfkalsdf/mapserver/0
In this case, it will add a single layer to the webmap .. enabled and configured popup... popup window WORKING in this case..
Thanks for bearing with me..
Cheers,
Srikanth Dasari