I have found that if I move the holes to fall wholly within the boundaries of the part, create the drawing and the hole table and specifically select those holes (not the front face, select the edges of the holes), then save the drawing and the part.
THEN move the holes back to be where you really want them, it works. At least it does for me in SW 2015.
EDIT: Adding a picture:
That sorted it. Thanks. Shame it has to be such a long way of doing things.