If you used 3x3 cell, it mean that folding is not the same as for 4x4 cell you mentioned in the very first post of yours. For 3x3 hexagonal cell, K-point of the hexagonal primitive cell is folded on the Gamma point of the 3x3 unit cell. And this is what is seen on your band structure plot. Band folding is a fully geometrical thing,not dependent on density functional, basis set, pseudopotential etc.
I would suggest reading some textbooks on Solid State Physics about how the Brillouin zone (primitive cell in the reciprocal space) is defined, in particular, reciprocal lattice vectors, how it depends on the size of the unit cell (lattice vectors) in the direct space. You may also take a look at this paper: "Extracting E versus k effective band structure from supercell calculations on alloys and impurities"
Voicu Popescu and Alex Zunger, Phys. Rev. B 85, 085201 – Published 2 February 2012.