Do you have a Ship To id on the SO. Check the sales order person on the ship to id. If you have the territory locked and a change to Sales order person for the territory then Ship To will not update to reflect the new sales person unless it gets updated.
Last time we had a territory re-alignment we did a DMT to update Ship To territories.
We have the same problem with quotes (we may have it with orders too, but it doesn’t affect anything for us there).
I have assumed that we’re missing some logic somewhere in how the sales person is assigned, but rather than deal with it we put in a BPM to force the sales person to be the one set against the customer. If someone does know how it’s meant to work, though, it would be nice to know.