The entire content of the window flickers white (But not the titlebar, because it is managed by the compositor/shell). The intervals are irregular, sometimes very fast flickering, sometimes less.
It is playable but really annoying.
Maybe update LWJGL to v3.x.
Environment
Fedora 23 (x86_64); Fedora Rawhide/24 (x86_64) all other distributions using Wayland
GNOME Shell 3.18.0+
xorg-x11-server-Xwayland 1.18.0
Is this still an issue in the most recent versions (currently that is 1.10.2, or 16w42a) of Minecraft? If so, please update the affected versions and help us keeping this ticket updated from time to time. If you are the owner/reporter of this ticket, you can modify the affected version(s) yourself.