The change you are seeing is due to the parasite drag model and its dependence on Reynolds number.
In addition to specifying alpha and beta, you also specify Recref -- a reference Reynolds number. That is used in conjunction with the reference chord and reference velocity to figure out the local Reynolds number (based on local chord and local velocity) across the model. That Re contributes to the parasite drag contribution.
Make sure all of your inputs are self-consistent.
Rob