I suspect that what is going on here is that the query you are using has been cached. When you make the query after you have modified the database (presumably by doing something like opening up SQL Server Management Studio and manually adding a new row), the PersistenceManager sees your query in the query cache and gets the items from the PersistenceManager cache.
If you want to see the new changes, you should use a QueryStrategy of DataSourceOnly, that will override the fact that the query is in the QueryCache.