I am currently using Web App Builder 1.1 Developer edition.
When I import my web app from my AGOL account, I can modify it, etc. I can then save the map, it downloads the zip of the application, and I then deploy it on my web server. The app works just fine.
When I modify the app by adding a custom widget, and follow this process, the web app does not work fine in deployment. The app now re-directs to an https and times out. The load screen shows, and then the redirect happens and the app never starts up.
When I view the customized app in web app builder, using the "launch" button, the app loads just fine, and the widgets work, etc.