Baseboards and rooms recompute walls moving walls between levels

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I have built my whole house in SH3D. I have come across a problem with some of my walls. I have built a wall from the ground floor the whole height of the building. Sometimes if I build rooms and use the recompute walls options, or use the new baseboard options, it resets the walls from the upper floor... i.e. it shifts the wall from starting on the ground, to starting on the top floor. Is this normal? Is it a bug? Thanks