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What extrude type are you using and what underlying terrain data are you using?
Right click on the layer properties in GoogleEarth and ensure the 'Altitude' setting is correct for the extrusion type you have used in ArcGIS (i.e. If you have extruded to an absolute height relative to sea level in ArcGIS but then have the buildings relative to ground in Google Earth, then that would result in incorrect heights)