Damned I had not keept the 3Dm ...but...refound a new example!
Jut a Solid Cube
a sphere at the corner
Boolean Diff
Fillet 0.2

Exactly same result than mine above!
don't works for the selections shown???
Beta 2.0 21 September 2008
I don't take care of the sphere's pole!)

Edit: Seems that is something like that!
I rotate the sphere and that works!
The problem is that the default drawing of the sphere is on the false position ;)