The stats say that 40 urls are reported and that 11 have been indexed, what about the other 29?

Found urls (40) are all urls encountered during the indexing process, including those linked to, for example, remote sites.

Indexed urls (11) are those that match the criteria defined in asearch.cnf.

You might have many links to pages that are never indexed. The reason why Alkaline stores them is that your index criteria might change and you do not want to make a clean index all the time. Thus any valid index can be reused at any moment for any configuration.