Like Herb, I think the thickness difference is most likely the problem. You cut the thick one first,then the 3/4 second. If you didn't readjust the bit height, it will make a different cut. Unexpected results are mostly forgetting something in the setup. I often mark the area to be removed in pencil so I can visually check how the bit lines up (see pix).
Don't forget that 3/4 ply isn't 3/4 and even milled hardwoods are not necessarily exactly 3/4, which suggests being meticulous about setting up each new cut.
The more I do, the less I accomplish.