I am using a system with Intel HD Graphics 2500 (Ivy bridge) and I have a little problem when playing Minecraft. Sometimes, my screen flashes blue, but only for a second every once in a while. Every 10 seconds or so, I see the flash. It only happens when I move or shortly after I move. If I stay absolutely still, it never happens. It happens with both OpenJDK 7 and Oracle Java 8. I have checked the X11 logs and have not found anything strange. I have experimented with every Minecraft setting but have yet to find anything that works. Also, I have noticed that the flickering does not happen if I make the window small. What is going on?
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.