Hi, wudnme. I'm going to hazard a guess that the problem may simply be that that portion of the edge is still more obtuse than the angle of the Sharpmaker -- it is very typical of factory edges to be more obtuse near the tip.
Since the Sharpmaker removes metal pretty slowly, unless you've got the diamond sleeves, you may want to reduce the angle of the primary edge bevel where it isn't getting sharp using a benchstone or other faster sharpening method. Then go back to the Sharpmaker for finish sharpening.
FWIW, your technique of keeping the edge consistently perpendicular to the Sharpmaker rods is exactly what I do ... if you didn't, you'll be sharpening at different, unknown angles along different portions of the edge. Zeasor makes a good point, too, that you also want to keep the "stroke" from becoming too horizontal or parallel to the edge.
Also, because the Sharpmaker rods are relatively fine grit -- about 800 equivalent for the medium, 1200 for the white -- it does work pretty slow, and it's easy to start using excessive pressure out of frustration. This can easily weaken the steel behind the edge, making it hard to get a good edge, and poor edge retention, and also can round off the tip. So IMO either the diamond sleeves, or another means of sharpening that's much faster, is needed if a blade is really dull or has sustained some damage. The Sharpmaker is at its best as a touch-up or finish sharpener, using very light pressure to produce outstanding edges.