Random screen flickering with Minecraft and Intel graphics
Solution 1:
Try this simple solution before reinstalling/changing drivers/changing java runtime/settings/etc.
Resize the Minecraft window to be just a little less than fullscreen. This solved the screen flashing problem for me, running Minecraft on Ubuntu.
Solution 2:
Install Intel drivers for Ubuntu: https://01.org/linuxgraphics/downloads/2014/intelr-graphics-installer-linux-1.0.7 it will solve your problem and you will see an fps improvement.