If I understand the problem correctly, Top, you're spot on here. The chamber has four corners in contact with your dick, but only two screws. The screws put all the pressure along one side of the chamber, so it applies most of the force along the line on one side of the chamber, rather than along both sides. That is, the little rubber chamber isn't all coming down evenly along your shaft. One SIDE of that chamber is biting down while the other is just sort of dragged along for the ride.
If you add two more screws to the other side of the chamber it should apply force more evenly. DLD mentioned this to me, that another member had done just that and it apparently made a world of difference to the comfort level. I've just been too lazy to do it myself and now I'm using the SiliStretcher instead.