Do you have the drill guide block set at the 3/4" and the depth collar set to the 3/4" mark. From the sounds of it you have one of these two things set incorrectly since the drill is not going deep enough. One easy trick is that you can run the bit through your jig with no wood attached and your bit should be just short of touching the base by about 1/8" or so. Hopefully this will solve your problem.
Unfortunately I am using coarse screws. I'd love to be doing something obvious and easy to correct.
I'm a little suspicious of the angle the screws are entering the board. The entry point into the board being joined is slightly below center. I've had some splitting occur and the screw never really tightens. I tried using the next size screw, 1.5 inches, and it held better but the tip protruded slightly through the board.
I've also been messing around with hemlock scraps with much better, although not perfect, results, Even using hemlock, which is fractionally thinner than the pine, I am getting occasional splitting and screws that don't seem tight.
This is making me crazy.