Just chiming in here - same issue since 3.3, same fix (switching to Windowed, then back to Borderless). A few FC mates have mentioned this as well.

To add a bit more, when I switch to Windowed, my entire game window actually disappears until the setting reverts. Can't alt tab back, nor does clicking the FFXIV icon on taskbar do anything, but when it reverts, I'm in Borderless Windowed until I exit the game again.