I'm not sure why we would create self-intersecting polygons, but it's not good! In this case, can you try using FME2013. I know it's not released yet but...
1) The Chopper polygon-chopping has been vastly improved
2) There is a new GeometryValidator transformer to repair bad geometry
You could certainly report this to the support team, if so please include your data so we can test it for ourselves in 2013.
Regards
Mark
Mark Ireland | Product Evangelist
Safe Software Inc.
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thanks mark,
I did try 2013 and either don' thave teh validator set correctly or it is not working as you indicate it could. I also submitted a support request for this.
The file tha tI get using th e passed only port still has the same repaired features when I run repair geometry on it in arcmap. I don't get anything out of the repaired port.