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Fusion Tables is an experimental app.

Fix: Polygons not showing on the map

I only see points; where are the polygons? 

Zoom the map in. Polygons are not shown at zoom levels 5 and below due because the complexity may not be representable within the available pixels without simplifying the shapes.

You may wish to use the Google Maps API and JavaScript to limit the zoom levels available on your map. Here's an example

 

Some geographic features are missing polygons. 

Multi-geometry. The ten largest-area polygons found in a multi-geometry placemark will be displayed on the map. Remaining polygons will not be displayed. Break multi-geometry placemarks into multiple rows if needed. 

KML is too big. A cell of data in Fusion Tables supports a maximum of 1 million characters; if you have more than this, you need to simplify the polygon or line or reduce the precision of coordinates in order to fit the description data into the 1 million character limit.

 

A few polygons disappear as I zoom in or out. 

Confirm the polygon is described as a counter-clockwise list of points, per the KML standard. Not all KML generation software does this correctly. Fusion Tables does a best-effort to display the polygons, but this will sometimes fail at particular zoom levels depending on how the shape falls across map tile boundaries.