Two other ideas come to my mind since these are 2/4's and the left side, which I assume you are screwing first does not have this issue. My drill driven screws easily over compress pine in the first joint which can cause a very slight out of square and make the other end more difficult to get straight. So, don't drive the left side tight at first ( only snug). The second idea is that your drawing shows an upward cant. In my experience this is not hole alignment, but torque on the side of the screw as it enters the hole. Dumb as this may sound, try using some liquid soap on the screw as a lube before you drive it. This will reduce the torque component of the screw on the wood and not impede tightening the joint. If you are using two screws, I would drive the bottom one first. Also, I would use GRK screws. They have been vastly superior in my experience.