Hi githorn,
I suspect that it could be related to the precision of the coordinates, this would likely explain why your unable to detect see them in the GeometryValiddator. If you are using CityDoctor to validate your geometries there is no was to set the precision for validation - other tools like val3dity let you set a precision for checking geometry issues, you could see if the geometry issues are present with val3dity as well as the tool you're using (I think by default it uses 5). You could try using a CoordinateRounder in FME to set the precision to three decimal places. If you are using a reprojector anywhere in your workflow then the precision will likely be 9....
The CoordinateRounder should go at the end of the workflow before the writer.