Badly made hub maybe, or bearing not seated correctly? Without looking at the hub and the bearing arrangement it would be impossible to say.
You could measure the overall hub width & see if anything is amiss there.
Ah was gonna say… not the wheel build itself cos the alignment is basically set by the bearings & spacing from the dropout.
Maybe the freehubs are subtly different.
Not missing a spacer on one of the hubs maybe? Otherwise there shouldn’t really be enough of a difference between hubs to completely throw out the shifting
They’re all 11sp hubs, with the same 11sp cassette, which I took off nice and cleanly, then reinstalled.
I’ve been swapping cassettes for years without this problem, it’s really annoyed me!!!
It’s a whole cog different - I cannot get down to the 11T sprocket with one of the wheelsets, and it jumps all over the top three.
Have you measured the relative distances between the dropout contact point and the beginning/end of the freehub? First validate there is a difference (which from what you say there probably is), as once you have factual evidence you could maybe contact the manufacturer. Is it just one wheelset that is out from the others?
I don’t think this is too unusual with three different hubs; I have to index gears when swapping wheels sometimes - if you find out which one is out you could shim the back of the cassette so they’re all consistent