Given two databases, 'foo' and 'bar', with entities in /Entities/Foo/ annotated as follows:

/**
 * Test
 *
 * @Table(name="foo.test")
 * @Entity
 */

Create an EntityManager instance with

$connectionOptions = array( 
    'dbname' => 'Foo', 
    'driver' => 'pdo_mysql', 
    <..etc..>
);

Use EntityManager#getClassMetaData( "Entities\\Foo
Test" ) to pass to SchemaTool#createSchema() and Doctrine appropriately creates a database table foo.test

Use EntityManager#getClassMetaData( "Entities\\Foo
Test" ) to pass to SchemaTool#updateSchema() and Doctrine fails with Exception
-> SQLSTATE[42S01]: Base table or view already exists: 1050 Table 'test' already exists

Inserting

die( print_r( $fromSchema, 1 ) . print_r( $toSchema, 1 ) . print_r( $schemaDiff, 1 ) );

into Doctrine/ORM/Tools/SchemaTool.php line 632 shows $fromSchema outputs

[_tables:protected] => Array
        (
            [test]

but $toSchema outputs

[_tables:protected] => Array
        (
            [foo.test]

which causes $schemaDiff to output

[newTables] => Array
        (
            [foo.test]

In summary, Doctrine/DBAL/Schema/Comparator considers foo.test a new table, because Doctrine/DBAL/Schema/AbstractSchemaManager lists its table as "test" rather than "foo.test".