I had the same thing happen - but it was only in our mystcraft mining age. Highly annoying, but since it went away when i returned to the overworld, it was manageable.
*sometimes* i could get it to go away by doing a 'reset video setting' in optifine. but that was usually temporary.
best option, is to use mystcraft to create a mining age, and put all your quarries there. Then you only get flickering when tending your quarry, and not while working in your base.