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Dynamic Analysis Question

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For those of you who are dynamic analysis experts, or have had substantial
experience in this field, here is a question:

We have a structure that is comprised of an irregular midrise tower (say 15
stories) utilizing moment frames located on top of a low rise, substantially
rigid base (concrete shear walls). Originally the building was dynamically
analyzed as two separate sections. In the first run the tower was assumed to
be a separate building located at grade and in the second run the forces
from the tower were applied at the top of the base and then analyzed. This
appeared to be crude approximation of the building behavior. So another run
was performed modeling the building as a whole. 

As one might expect when the building is analyzed as whole, a substantial
portion of the forces induced by the base is getting dumped into the tower
and penalizing the tower frames.

The question is which one is more realistic? Is there a middle ground or
better alternative?

Thanks in advance

Ben Yousefi, SE
San Jose, CA