Okay, first the file you uploaded has already had the circular fillet applied and the fillet is no longer there so I can not go backwards. What I need in the file BEFORE you do the fillet!
Second, why are you using a circular fillet in the first place? Why not start with a nurbs cylinder and then do a "Edit nurbs > Round Tool"?
Anyway, I cannot reproduce the problem you are having but because you are doing it in a strange way I am still not sure if it is something you are doing or if you have a maya problem.
Also, your version of Maya is the student version so that could have something to do with it. In any event I have to run out for a while when I get a chance I will post something about Fillets vs Rounds and Trims and Trim Convert.
"If I have seen further it is by standing on the shoulders of giants." Sir Isaac Newton, 1675