To start, I doubt the knife's angles are the same as the sharpmaker's (that 40-30 stuff seems more appropriate for outdoor knives and the like anyway), so you probably are just scraping the side of the bevel somewhere with it. Are you sure it has the same angles on both sides? Some double sided Japanese knives come with 70/30 or some other ratio bevels, and you can't do those on a Sharpmaker anyway (I only use my Sharpmaker on my Wushof's and Hecknel's... the 30 degree setting sharpens those up nicely, though I think they come with something closer to 22-25 degrees).
Generally, what I do is grab a 2k or 5k waterstone (depending on how sharp it seems in the first place) and sharpen it up a bit using the existing angles (you can rock the bevel on the stone, or sometimes go by visual clues in the water, to tell when the bevel is flat on the stone and just use whatever angle that is without caring what it is). If the edge seems too fragile, then I may drop back to the 1k and raise the spine just a smidgen and give it a slightly thicker bevel, but mostly I haven't had to do that.
Grouch, I have a table of waterstone grits (Shapton, old JIS standard and current JIS standard, Norton and DMT http://members.cox.net/~yuzuha/jisgrit1.html but bond makes a difference too since, while Norton says their 8k actually uses abrasive of a size equivalent to Shapton's 4k, everyone says it actually leaves a finish somewhere between the Shapton 5k and 8k), but it doesn't have sharpmaker rods in it... think that was CBWX34's spreadsheet.
Here is a photomicrograph of the Sharpmaker ultra-fine (comes with the medium and fine rods so I ordered a set of the ultra-fine too)
(25x objective, about 1,400x total). There are some larger and quite a few smaller (plus the tips of larger grains poking out of the matrix), but the majority of the larger grains appear to be around 2,000 grit JIS. But they are rounded and held tightly in a very dense matrix so they do not cut at all like a waterstone. Instead, they burnish like an orange stick on modelling clay, and, also like smoothing clay with a stick, the rods seem pull loose little balls of metal and smear them over the surface and leaves a finish that looks like this:
Leaves the burnished part nice and bright the surface isn't exactly smooth. Here is the same hunk of metal that I polished on a Naniwa 10k at a right angle to the sharpmaker that exposes the gouges made by the balls of metal the sharpmaker pulled up:
Anyway, while the UF rods are probably 2k-3k grit abrasive, they do seem to leave a 5k-8k finish in the smooth burnished parts (the gouging/streaking makes them unsuitable for polishing the sides of blades but that should be less of a problem on a thin edge bevel).
mi hatenu yume no
(This final scene, I
I will not see to the end.
My dream is fraying.)