I've had a few occasions where File Explorer dialogs (e.g., "overwrite existing file?", etc.) pop up behind File Explorer itself. Normally I use short, wide File Explorer windows, so I usually see a small part of the dialog between windows - and of course it flashes the icon on the Taskbar.
I've heard others are seeing this as well.
Has anyone found any good workarounds for this errant behavior yet in Windows 8.1?