As with Fallout 3 it won't work it you use a preset for your face as the save file won't contain any face gen data, just a reference to what preset you are using.
If you have a save file that doesn't work then reply to this thread with a link to the save file and I'll have a look at it.
I case you are wondering I haven't actually worked out the save file format I just search for your character's name in the save file and the face gen data is either 2 bytes or 10 bytes beyond that. (I can however find and change the S.P.E.C.I.A.L. data :hubbahubba: ).