The high end of the step wedge is where it is important to know the correct values. That is where the speed point will fall. My densitometers calibrates to a standard around 2.0, so when I measure my step wedge in the 2.0 range I know pretty well that the densities I'm using are correct.
So, with unknown high densities on wedge and the addition of extra density, you could easily be 1/3 stop off in the calculations of the light reaching the film at the 0.1 point, thus giving you the wrong speed.
That is interesting that the step wedge is between glass. On my EG&G, and the description in the manual, the plastic chamber ("gray scale box" per the manual) has a clear glass on top.
On my Wejex, the step wedge is also between glass, but the top of the platform, on which the glass resides, actually fits under the arm of my Tobias densitometer. Maybe they planned it that way because both devices are made by the same company.
Extra agitation or development should have minimum effect on the speed point, so I am suspecting errors in measurement of the step wedge density. But just speculation at this point.