This usually happens because the missing images have a "Rejected (x)" rating. Any time you open the Filter HUD, whether in a Project or Smart Album, the rating will default to Unrated or Better until you change it. A reject ranks lower than unrated, so your search results will react accordingly.
If you want all images to be eligible for search results, remember to pay attention to the rating that you are specifying. Move the Rating slider to the left so that you have "Rating: is greater than or equal to x."