Thanks for the more detailed workflow information. I agree that nothing stands out there as a likely culprit. I have a Durst 138 also, and it does hold focus very well. What format were you testing? Your enlarger is set up with the condenser head? I don't understand the focus lever on the lens. Is that to open the aperture?
I thought you must be focusing with the lens open since you are able to focus by eye. That doesn't explain the problem, but is certainly not the normal way to use a grain focuser. I wouldn't expect that much focus shift, and that still wouldn't explain the situation, but it is certainly a variable I would eliminate. Another variable to eliminate is the test negative. I can think of no reason that would be an issue, but I would focus using a real negative, focusing on the grain at working aperture since that is what you will do when making photographs.
I have used a lot of grain focusers over the years and never seen a single issue like you describe, so have trouble imagining 3 (or is it 2 - not entirely clear) that don't work. I see very slight differences between my Critical Focuser and my Microsights, but I mean barely detectable. This could easily be down to adjustment, or just tolerances.
Ctein's book (linked above, I think) describes a way to test focus accuracy while eliminating many of the variables here.