Hi Jianxia
Can you confirm please if this bug was indeed supposed to have been fixed in the WAB Developer's edition 1.1?
I'm experiencing very similar problem using 1.1 - I have a web map with pop-ups enabled (the pop-ups in this web map work fine in AGOL, and also in a web app built using WAB Dev beta 3 edition) where none of the pop-ups appear to work in a web app built using WAB Dev edition 1.1.
All layers are enabled in the web map by default.
Cheers,
-Paul