legacy Open Studio - Energyplus geometry problems

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It looks like your origin just isn't at 0,0,0. Notice how no vertices have zeros for all values. Both x and y have non 0 origin.

If you look at Obj2 (the hidden wall we can't see on the left) the x value is -0.0958. If you measure from there to 3.1042 you get a length of 3.2 meters.

The lack of 0,0,0 origin shouldn't be an issue, but you could manually fix it by slideing the group, then go within the group and select all and move the geometry to the desired location. If you were using the newer OpenStudio there is a user script to clean up origins that moves the space origin to one of the floor surface vertices. It was made so that another script can infer building stories based on zone origins.