I noticed the exact same thing. However, I finally found the theater by putting in the exact zip code (of the theater)...then once I found it, I added it as a favorite.
That took care of the theater I typically go to. However, I'm now worried about it not finding nearby theaters when I'm traveling or on vacation.
In the big BoxOffice thread, the dev said that the listings were limited to what was available via Fandango.com. Check out that site and see if your theaters are listed. If not, have the movie theater manager e-mail them at listings@fandango.com to be added to the database.