I have an alignment conundrum. I have scenario where when the frame is alignment HT to dropouts (according to Park tool and to center-line check with height gauge on alignment table) the rear wheel is skewed 3- 4 mm from frame in one direction. That is, the wheel is parallel to the frame line but off-center to one side 3-4 mm. The center-line on my DA is at the same height as the center line of ST and HT. AND the thru-axle is both perpendicular and parallel to the frame at BB and ST within 0.3 degrees. The dropouts are also parallel to the rest of frame within 0.2 deg. as best my angle finder can do.
Is 0.3 degrees enough to make 3 - 4 mm difference at the outer edge of a 29’er rim?
I’ve been at this all day, totally baffled as the cause. I don’t know what to chop, re-do, fix, without knowing the cause…
Anyway, I guess I’m hoping someone has a “Once when I… the rear end was wonky and I found that… fixed it”… or, “Hey, moron, did you remember to check… compare the … with the … obviously”
either is fine 
And NO I don’t have another wheel to try on hand. I could maybe find one…