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I am reasonably sure that it is seated properly on the hub. Laying awake at night wondering what is causing the alignment problem ...
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I would agree that it is most likely seated evenly, but, maybe not properly.
If you had an alignment problem caused by an obstruction, where the rotor was "cocked" to one side it will still rotate true and will contact part of the pad all the time.
I believe you have two problems:
1. The hub seated either early or late. for some reason your rotor is either farther in or farther out than it used to be.
2. The rotor is slightly warped. You likely didn't realize it when the rotor was positioned properly within the calipers.
Another problem could be that the caliper is not properly seated causing it to rub. (the rotor would still have to be warped)
check which pad is rubbing (the inner or outer) and that will let you know whether the hub is too high or too low. Then fix whatever is causing it, (Improper bearing seating, dirt, wrong bearing, etc.)
If it were me, I would try to determine if the rotor is out of true. (anyone who turns rotors can tell you) If it is, it might be possible to true it by turning it. Worst case, replace it even if it isn't still rubbing. It will cause a hot spot on your rotor and that certainly is less than good.
Mike