have you used qiagen? if so, they recently introduced LysBlue. when P2 added, make sure that the P2 buffer mixed well without any white patches. same way, when P3 added, the complete decoloriztion of the lysate making sure the mixing of P3
That can happen simply because your samples have different amounts of cells.
Blue color is proportional to the level of cell lysis, so if one of your samples has less cells to begin with you'll necessary have a lighter blue color.