doctrine orm:validate-schema failure when using Migrations

I'm using Doctrine 2.1.2 with Migrations 2.0. Doctrine cli tool works
correctly for both schema creation (from annotations) and migrations
but, after using the tool to validate the schema i get the following
error:

[Mapping] OK - The mapping files are correct.
[Database] FAIL - The database schema is not in sync with the current
mapping file.

The failure is caused by the doctrine_migration_versions table that
the migration project has created in the db of my project.

orm:validate-schema fails because the relation is not defined as an
entity in the annotations.