A definition query is a common cause, and so may your symbology, and both may be a common source of irritation, at least to me. I wish the nanny software allowed the layer to appear with only a warning that new features may not appear.
Hi there! Are you referring to feature templates? One thing though, feature templates available on the create features window are only for those feature classes added on the map document before an edit session is started. Meaning, if you add another feature class after starting an edit session, its feature template won't automatically appear on the create feature window. You still have to add it using the organize template.