I'm having an issue very similar to this one. (TheTrueMayhem: I have a workaround too, read below.)
When creating a new project, if I select one of my custom databases as the "base" it is created without tables, and the file size of the new database file (e.g. "test.db") is only 3 kb. The original database is 21,206 kb.
However using the "Unmodified Hal 6 Default Brain Database (Backup)", or some of my other custom databases, works without a problem.
Workaround: If you're making a new brain (for example, called "test"), delete the tiny database file (in my example, "test.db"). Create a copy of your base file, and rename it (here, to "test.db").
Hope this helps,
Grant