One thing to consider is that your stock may not all be the same thickness. I have encoutered that where I set up the dado blade to cut the stub tenons, and I get one to fit great, but then the next is sloppy. If you can thickness plane all of the material at the same time, with the same setting, you should have good results. I usually cut my stub tennons with the rail laying flat on the table saw and use a dado blade to create the tenon, flipping the piece to make sure the tenon is centered. If your stock is all the same thickness, and you've centered your groove for the panel, your centered tenon should align pretty good (within a sandable amount). If you are using a regular blade to make the groove, you'll want a blade that leaves a flat bottom otherwise you wont end up with a joint as pretty as the one Bret posted.