JPA 2.1 spec permits registering of converters using @Converter annotation. This works ok, at least in EclipseLink's last version. But it doesn't work with XML-free configuration using Spring. This is due to DefaultPersistenceUnitManager class, which scans specified packages looking for classes annotated with @Entity, @Embeddable and @MappedSuperclass, but not @Converter.
Just adding new AnnotationTypeFilter(Converter.class, false) to entityTypeFilters field worked for me.