Solution to alignment problem
I had the same problem. The problem lies in the alignment stop on the left hand side of the jig. This sets the offset between the horizontal board and the vertical board. For the large jig, this is 1/2 inch. The problem is the manual says position the vertical board centered between the pins of the jig and then slide and lock the alignment jig against the vertical board, and you will have a stop for the horizontal board with the correct offset. The problem is the alignment stop doesn't lie perpendicular to the jig when you press it firmly against the jig. So this throws off the alignment between the top and bottom boards. The way I got around this is to position the vertical board between the pins and square it up using the dovetail template. Then remove the template and position the horizontal board perpendicular to the vertical one, and offset it 1/2 inch to the left. Lock these boards in place with the jig clamps. Then slide the offset stop against both boards and tighten the lock screw. You won't be square with the offset stop, but you only need to touch the boards in two points, one for the vertical board and one for the horizontal.
I don't know why they don't do a better job with this part.
Once you get this working, the next item is depth of cut. 1/64 can make the difference between a tight fit and a loose fit. After this is dialed in, then adjust the template position if needed forward or backward. If the depth is not right, you'll never get it dialed in.
Pain in the butt to learn to use. I must have made 50 joints before it made sense.
Sorry this is a few years after, but just bought mine and was searching for solutions myself.