When hair intersects with dupli instances, the dupli rendering becomes random, depending on position.
Test file (with short rendered sequence):
Render the short anim sequence to see the effect.
Animated hair systems moving through duplis (e.g. a sheep moving through dupli grass) thus cause flickering. Tests show that this is simply depending on the hair position though, the hair object does not have to be animated.
The error only appears in Cycles renders, but not Blender Internal or the OpenGL viewport.
My guess is that this is an intersection problem of BVH nodes with curve data.