This issue has been closed as 'Won't Fix' due to an extended period of time without updates. If this issue is important to you please let us know by posting on the AnswerHub or UDN, and Epic will re-open the ticket for further review.
UDN users are reporting the windows taskbar being on top of the game window when starting in windowed fullscreen. Seems it is related to an initial loading movie.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-20411 in the post.