When viewing in the tracking station not all craft are shown, only the craft type is shown that is selected. In previous versions I don't think this was happening, so just as a heads up if your craft seems to disappear in the Tracking Station check the craft type that you have selected.
Not sure if this was already posted, if so please feel free to delete if it's not necessary.
Castille7's post in Change Craft Description, Craft Disappears in the Tracking Station was marked as the answer