Yeah Subds have their little probs in the convert every so often.
I take it from what you're saying its purely in the switching to and from the SD surface.
Usually its a build up of history on the sub-D surface which is basically called blind data. These nodes do have their uses but in modelling they can cause a bit of trouble. To get rid of them simply go to the hypergraph with the model selected and graph the up and downstream connections. This will show you all the nodes attached to the geometry, from the actual shape node right down to any history.
If there are any blind data nodes visible, delete them. But make sure you have deleted all the history too on the model otherwise it may not work. Hopefully this is the problem and you should now be able to carry on. Also be aware that sometimes the model may just seem to disappear, this is one of Mayas little quirks, so simply check the Outliner and make sure its all there, select the model and re-apply a shader to it.
Another prob with conversions to sd's can be points that may not be merged or left over from a deleted edge or an edit. Run a cleanup from the Poly menu set, anything that is wrong will get hilighted.
Lastly, Ive not used Subds for a while since the intro of the 3 key command to convert to a smooth poly. Its just as good as good if not better as subds can become heavy once you start placing those level edits on them, so bear that in mind, and also texturing needs more attention because of the smoothing algorythm place on them too.
hope this helps