Minecraft apparently uses a resize request in order to become fullscreen which causes the window manager to not properly implement fullscreen unredirection. Fullscreen unredirection is needed in Gnome to improve performance and reduce latency when playing games. The current implementation causes micro-stuttering and forced Vsync in Minecraft.

The following warnings are triggered in the gnome-shell logs:

Mar 18 20:52:57 fedorapc gnome-shell[1542]: Window manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x6000009
Mar 18 20:52:57 fedorapc gnome-shell[1542]: Window manager warning: Treating resize request of legacy application 0x6000009 as a fullscreen request

This issue can probably be solved by sending a proper fullscreen request to the Gnome window manager. This would benefit a lot of users seeing as Ubuntu (which also uses Gnome) is one of the most used desktop distros. The micro-stutters don't make for an enjoyable experience when playing Minecraft.