Just a hunch, but I guess that error message might mean that there is some geometrical/topological errors? Maybe polygons that are not closed (even though you said you checked - what did you use to test that?), or duplicate points, self-intersecting polygons etc. 
Maybe you could check them with a GeometryValidator first, and repair them?
                
     
                                    
            Hi @bubblebeb This looks like a problem with FME.  Please submit a case if you can reproduce the problem in the latest release or betas.
                
     
                                    
            Hi @bubblebeb This looks like a problem with FME.  Please submit a case if you can reproduce the problem in the latest release or betas.
Thanks @danatsafe I have submitted a case for it.