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.
Suite 2017, 7445-132nd Street, Surrey, BC, CANADA
T 604.501.9985 | F 604.501.9965
| Twitter @FMEEvangelist |
http://www.FMEevangelist.com