Major Description
Whenever the last activity before releasing a store (with StoreConnection.release) is a write transaction, the entire database is empty the next time you create a dataset. I should note that this only happens when you start with a new index store. If you release the store after a write transaction on a store which was created the first time around where you did not end with a write transaction, the problem will not occur.
I attached a little test case which illustrates the problem. Just provide a new index location as a java argument (or hard code it)