I'd suggest calling Kreg Tech Support 800-447-8638
explain the problems your having, perhaps they may have an answer.
I'd suggest that the screws, when installed, are directed away from the edge of the drawer member, you're driving the screw into.
Hence, the pockets for the screws would be on the outside of the drawer sides, and pointed in an inward direction, away from the end of the mating panel.
When the pockets are on the inside surface of the drawer side, the screw point will exit toward the outside end of the plywood panel, which can cause the plys to separate.
Have you tried 3/4" long screws?