Hi, the issue is that Minecraft (Pi Edition) uses OpenGL ES to display all those blocks in 3D. At the moment there is no easy way to show OpenGL ES output within the Desktop. So Minecraft uses a trick. It creates a window on the Desktop and then places the OpenGL ES overlay in the same location. When you use an HDMI or AV monitor/TV on the Raspberry Pi the Desktop (which is just one layer) is displayed along with any other layers created by OpenGL ES, OpenVG, the Raspberry Pi camera, etc. When you use a GPIO display, the available driver creates a single (framebuffer) that is used to display the Desktop. The only way around this (that I know of) is to run the Desktop on the framebuffer that is displayed on the TV/monitor attached to the Raspberry Pi (/dev/fb0) and use the program fbcp
to copy everything displayed to the framebuffer of your GPIO LCD display (typically /dev/fb1).