Update to entity is not recognized or persisted when using guice-persist

Question

I am having an issue with guice-persist and guice-servlet (http-request scoped jpa sessions) where I attempt to update an entity's value and persist that update, but the update is never persisted to the database. I have tried forcing the write with an entityManager.flush() and entityManager.getTransaction().commit(), but when I look in the logs nothing seems to happen, even when the http session ends and the jdbc connection is released.
I would normally expect to see hibernate issuing a sql update statement, but the update never seems to register. What strikes me as odd is that I have no problem creating new entities, this only seems to be effecting updates.

I have a Singleton scoped servlet that has an injected UserDao, which uses an injected Provider<EntityManager>.

Here is my persistence.xml:

<persistence xmlns="http://java.sun.com/xml/ns/persistence"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://java.sun.com/xml/ns/persistence http://java.sun.com/xml/ns/persistence/persistence_2_0.xsd"
         version="2.0">
<persistence-unit name="db-manager">
    <provider>org.hibernate.ejb.HibernatePersistence</provider>
    <class>com.turms.server.database.DurableUser</class>
    <properties>
        <!-- Disable the second-level cache  -->
        <property name="hibernate.cache.use_second_level_cache" value="false"/>

        <property name="hibernate.connection.driver_class" value="com.mysql.jdbc.Driver"/>
        <!--<property name="hibernate.connection.driver_class" value="org.apache.derby.jdbc.EmbeddedDriver"/>-->
        <property name="hibernate.connection.url" value="jdbc:mysql://localhost:3306/TestService"/>
        <property name="hibernate.connection.username" value="xxxxx"/>
        <property name="hibernate.connection.password" value="xxxxx"/>
        <property name="hibernate.connection.pool_size" value="1"/>
        <property name="hibernate.dialect" value="org.hibernate.dialect.MySQLDialect"/>
        <property name="hibernate.hbm2ddl.auto" value="create"/>
        <property name="hibernate.archive.autodetection" value="class"/>
        <property name="hibernate.show_sql" value="true"/>
        <!-- Default is false for backwards compatibility.  Should be used on all new projects -->
        <property name="hibernate.id.new_generator_mappings" value="true"/>
    </properties>
</persistence-unit>

I have replicated this problem using MySQL and Derby databases.

Here is an example of an update attempt that fails:

public boolean testUpdate(DurableUser user) {
    entityManager.get().getTransaction().begin();

    String testUpdateString = "askdjfaskdjfalsdkf";
    user.setField(testUpdateString);

    entityManager.get().persist(user);
    log.info("user field persisted");
    entityManager.get().flush();
    entityManager.get().getTransaction().commit();

    entityManager.get().clear();
    return true;
}

It takes a DurableUser (created w/o issue in a previous http session) and updates a field. Even with an explicit flush() and commit(), hibernate issues no update statement.

I noticed in the logs that org.hibernate.internal.util.EntityPrinter does log the user's toString(), which shows the updated field. Would that mean hibernate does recognize the entity has been dirtied and is still not persisting the changes?

Can anybody answer why I can successfully create new entities but not update existing entities? I'm completely stumped so far.

EDIT: Here are the logs from the session:

2013-12-04 20:56:10,881 DEBUG http-apr-8080-exec-7    spi.AbstractTransactionImpl - begin
2013-12-04 20:56:10,881 DEBUG http-apr-8080-exec-7           jdbc.JdbcTransaction - initial autocommit status: true
2013-12-04 20:56:10,881 DEBUG http-apr-8080-exec-7           jdbc.JdbcTransaction - disabling autocommit
2013-12-04 20:56:10,881  INFO http-apr-8080-exec-7                    dao.UserDao -  user field persisted
2013-12-04 20:56:10,881 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Processing flush-time cascades
2013-12-04 20:56:10,881 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Dirty checking collections
2013-12-04 20:56:10,882 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.cards#7], was: [com.xxx.server.database.DurableUser.cards#7] (initialized)
2013-12-04 20:56:10,882 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.donations#7], was: [com.xxx.server.database.DurableUser.donations#7] (initialized)
2013-12-04 20:56:10,882 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.installments#7], was: [com.xxx.server.database.DurableUser.installments#7] (initialized)
2013-12-04 20:56:10,882 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Flushed: 0 insertions, 0 updates, 0 deletions to 1 objects
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Flushed: 0 (re)creations, 0 updates, 0 removals to 3 collections
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7             util.EntityPrinter - Listing entities:
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7             util.EntityPrinter - com.xxx.server.database.DurableUser{donations=[], installments=[], id=7, username=test, name=test testerson, passwordChangeKey=askdjfaskdjfalsdkf, cards=[]}
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7    spi.AbstractTransactionImpl - committing
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Processing flush-time cascades
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Dirty checking collections
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.cards#7], was: [com.xxx.server.database.DurableUser.cards#7] (initialized)
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.donations#7], was: [com.xxx.server.database.DurableUser.donations#7] (initialized)
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7           internal.Collections - Collection found: [com.xxx.server.database.DurableUser.installments#7], was: [com.xxx.server.database.DurableUser.installments#7] (initialized)
2013-12-04 20:56:10,883 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Flushed: 0 insertions, 0 updates, 0 deletions to 1 objects
2013-12-04 20:56:10,884 DEBUG http-apr-8080-exec-7 .AbstractFlushingEventListener - Flushed: 0 (re)creations, 0 updates, 0 removals to 3 collections
2013-12-04 20:56:10,884 DEBUG http-apr-8080-exec-7             util.EntityPrinter - Listing entities:
2013-12-04 20:56:10,886 DEBUG http-apr-8080-exec-7             util.EntityPrinter - com.xxx.server.database.DurableUser{donations=[], installments=[], id=7, username=test, name=test testerson, passwordChangeKey=askdjfaskdjfalsdkf, cards=[]}
2013-12-04 20:56:10,886 DEBUG http-apr-8080-exec-7           jdbc.JdbcTransaction - committed JDBC Connection
2013-12-04 20:56:10,886 DEBUG http-apr-8080-exec-7           jdbc.JdbcTransaction - re-enabling autocommit
2013-12-04 20:56:11,613 DEBUG http-apr-8080-exec-7 internal.LogicalConnectionImpl - Releasing JDBC connection
2013-12-04 20:56:11,614 DEBUG http-apr-8080-exec-7 internal.LogicalConnectionImpl - Released JDBC connection