The Pre-Stress input to Modal calculates a new stiffness matrix from the solution of the Static Structural model. The axial tension causes the stiffness matrix to change significantly and that is seen in the Modal frequency. It seems the moment load does not change the stiffness matrix.
I believe the way Pre-Stress works is that it only uses the stiffness matrix, but it does not update the shape of the part prior to running Modal. Try to put a huge moment on a straight beam so that the deformed shape is a semicircle and see what happens in the Modal analysis.
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