Even if the frame was totally out of alignment the wheel would be in the same axis than the derailleur. Only thing I could think of it's the wheel having the wrong end cap with all the different standards going. Other than that maybe go to a shop and have the derailleur problem tested.
Thanks for the suggestion but I’ve used the wheels with another groupset on the same bike and had no problem shifting with that and haven’t changed the end caps.
Even if the frame was totally out of alignment the wheel would be in the same axis than the derailleur. Only thing I could think of it's the wheel having the wrong end cap with all the different standards going. Other than that maybe go to a shop and have the derailleur problem tested.