Activating fullscreen mode in Windows 10 appears to change something about Scrivener’s process, which makes it appear to not be running on the taskbar.
Normal window, not fullscreen:
After entering fullscreen mode:
Note that clicking Scrivener’s icon when in fullscreen mode changes the process name back to that of the active project and, after an unusually long wait, does refocus the program.
Reproduced on Windows 10 Home Edition, Scrivener Version 2.9.0.4 Beta (149671) 64-bit - 30 Mar 2018