I don't fully understand why it creates these extra polygons that are both sided and are a nightmare to get rid of later on...
Last time I did this and it was a bad dream, I had to separate the piece and all polygons attached to it.
The it was a matter of breaking down the now object by cutting magically to get rid of the reverted planes and make sure I did not destroy the original one sided plane.
Once you see this, do not click to cut... :P try moving around till you find an overlap which doesn't create extra triangle.
It could be because of the way I generated the planes sides in the first place.
As this is my first time doing it, I wouldn't be surprised if I have to scrap this and start over again. :P