It`s not the diaphragms. Old school hand calculation methods like the portal method and the spurr method are approximations. They are, in general, inexact. As an example, the portal method assumes that all of your columns have inflection points at mid-height. In reality, that`s almost never true. At the same time, it`s often pretty darn close to true.
So long as you`ve nailed your input, FEM software will always give more exact answers. The portal and spurr methods are invaluable for both preliminary design and FEM output checking however.
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