Revit has a setting when you select a level, that it can be classified as a Building Storey or not. If it is, it will appear in the Snapshot total for the Number of Building Stories. If you do not want a level to be included (eg. Foundation level, Parapet Level, etc.), uncheck this setting in Revit.
Settings in Revit will affect the information sent to the Excel Snapshot such as the Project Address, Site Location etc. Settings used by FenestraPro such as custom properties which have been set for glazing may not appear in Revit but may show in the Excel Report as these are being used for the purpose of Energy Analysis.