By default CAESAR II uses the "other" equation for the Expansion Stress Allowable:

Se = f(1.25Sc + 1.25Sh - Sl)

You're seeing different allowables through out your system because Sl is varying. If you don't want to use the above equation, uncheck the "liberal allowable" item on the "Special Execution Options" dialog.

This is the whole point of this thread.