Hey Verne, I have had some similiar issues with alignment. Every once in a while, driving the screw seems to separate the pieces. Here’s the solution I came up with and it’s worked for me so far.
After I get the pocket hole drilled I switch bits and enlarge the narrow section of the pocket hole just enough so that the screw I’m using slides all the way through without biting into the pocket hole. If you set the collar just a hair deeper than the set up jig calls for the tip of the bit will punch through just enough so you can do this coming in from the back side. With the screw spinning freely inside the pocket hole it actually acts like a clamp and draws the two pieces together.
I’ve also found that if I’m going for super perfect it helps to clamp the pieces together dry, start each screw a thread or two just to mark the location, then take it all apart and drill shallow pilot holes to get the screw started in the second piece. You have to make an educated guess at the angle when you’re doing this but it doesnt’ have to be perfect.
When you do this you have to pay extra close attention to the length of screw that you choose because the tip of the screw usually ends up a little closer to the surface of the piece that you’re screwing to. I typically pick a screw length shorter than what the charts recommends. This keeps the tip far enough away from the surface that I’m not worried about sanding through and so far it hasn’t seemed to affect the strenght of the joint.
It’s some extra effort but it has solved the alignment issue for me every time. I think the issue would go away if Kreg were to make the tips of their bits just a tad bit longer and wider but unitl they do, this is how I deal with it.
-- I've cut that board three times and it's still too short!