ok raywind. when you convert it back to poly you will see that those circles are extracted/single polys. your geometry got broken. just grab one of the circle´s vertex, move it and you will see.

look at this 3 pics here. the first one is a single geometry consisting if 2 faces. when you convert it to subD you get the second geometry. but if you let´s say duplicate the first plane and cut from both planes the opposite face so it seems to be one object - you might even combine the 2 faces - and convert it to subD -> you´ll get pic 3.

cheers!