EI and EA factors deal with the residual stresses which remain in the structure, which will result in a change in effective stiffness.
The technical note for AISC360-05 Direct Analyis Method states that: " Reduction factors to section EI and EA are automatically applied by the program .... However, as soon as a design is run the reduction factors are used and remain in the model. This means that the first time the model is analyzed and designed, users must iterate between design and analysis at least one additional time. Thereafter, both analysis and design will have reduction factors applied automatically. "
You can try changing your "Analysis Method" from Preferences>Steel Frame Design Preferences to "Effective Length" and see how that works out.