Does anyone else have any issues with standard widgets (the layers and legend widgets) disappearing when you launch an application from the Home page? Interestingly this only happens the first time you launch an application. If you close and open the application again, the widgets appear. Only the standard widgets that disappear, not any of the custom ones.
Are you using the the Foldable or JewleryBox themes? If so there is a bug where the icons in the Header Controller are moved bellow the Header Controller widget bar and are hard to see.
When I tried to use the Foldable and Pocket theme through Web AppBuilder it would not keep the widgets that I created. Once I saved it and came back those widgets disappeared. I thought it was my network or my computer period so I had Joe Bayles check on his end and it had the same issue.