it could be the same bug I was expirancing with maya 4.5 when I converted SubD' to poly I got both a poly object and a nother one.. I was never really sure if the other object was a poly or subD.
In short even when I had it ticked to replace the object. I still ended up with more than one object in the same place.

it seems it happens with some peoples maya.. and others it dosn't.

I just look in the outliner for the converted object and delet the others.