Strange leveling problem by PrusaI3
The Prusha I3 design uses two rods to guide the Y axis, which moves along the rods on linear bearings.  If the rods are not strictly planar, there will be movement of the bed as it moves to and fro.  You would not be able to correct this with the leveling screws.

Be sure that the rods are planar, and that there is no torque on the bed from uneven rods.  Even if the bed doesn't flex, the frame may flex if the rods are not planar.