windowed fs is bugged after June 6 update
This is almost certainly a windows related issue, not a gw2 issue. Recent Windows updates made some changes to how they detect “windowed fullscreen” applications, and those caused the taskbar to show above the gw2 app — and a bunch of other games too.
The most common cause seems to be running any sort of addon, overlay, etc, that draws additional windows on top of the game.