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Did you use the create spaces from diagram multiple times for each story? If you did then you would end up with extra stories as it always makes a new story when it is run, and then additional stories if number of floors is greater than 1. If you clear out all story assignments you can use the AssignSpacesToStories measure with apply measures now to re-assign the stories. It looks at the min z value of all of the floor surfaces in a space to group them by story. I believe there is a script in the SketchUp plugin that can do this as well.

Also for reference, the story object isn't directly used by the simulation and doesn't make it into the EnergyPlus model, but if you are going to run measures that add HVAC systems, they often make use of the story assignments so in that case, if it is helpful organizationally in viewing spaces, then it is important to fix.