Have you used Ellipse extrude or Scale Cylinder?

Works fine for me after a "scale" modeling a cylinder!
(boolean fillet and trim :)

Ps I have not used your file!

Thanks Petr, I have gathered this up with some other stuff to eventually send to the people who make the geometry library that I'm using, they will be the ones who will need to fix these ones up. It will probably be a while before that will happen but it is great to have failure examples on hand.

Thanks!

- Michael