Symfony2 Form with custom FormType calls DataTransformer with same data in both directions

By what I'm seeing in your transformer class you're not implementing the code right. This should be the correct implementation:

namespace App\YourBundle\Form\DataTransformer;

use Doctrine\ORM\EntityManager;
use Symfony\Component\Form\DataTransformerInterface;
use Symfony\Component\Form\Exception\TransformationFailedException;

class IdToMyModelTransformer implements DataTransformerInterface
{

    /**
     * @var EntityManager
     */
    private $em;

    /**
     * @param EntityManager $em
     */
    public function __construct(EntityManager $em) {
        $this->em = $em;
    }

    /**
     * Transforms a value from the original representation to a transformed representation.
     *
     * This method is called on two occasions inside a form field:
     *
     * 1. When the form field is initialized with the data attached from the datasource (object or array).
     * 2. When data from a request is submitted using {@link Form::submit()} to transform the new input data
     *    back into the renderable format. For example if you have a date field and submit '2009-10-10'
     *    you might accept this value because its easily parsed, but the transformer still writes back
     *    "2009/10/10" onto the form field (for further displaying or other purposes).
     *
     * This method must be able to deal with empty values. Usually this will
     * be NULL, but depending on your implementation other empty values are
     * possible as well (such as empty strings). The reasoning behind this is
     * that value transformers must be chainable. If the transform() method
     * of the first value transformer outputs NULL, the second value transformer
     * must be able to process that value.
     *
     * By convention, transform() should return an empty string if NULL is
     * passed.
     *
     * @param mixed $object The value in the original representation
     *
     * @return mixed The value in the transformed representation
     *
     * @throws TransformationFailedException When the transformation fails.
     */
    public function transform($object) {
        if (null === $object) {
            return null;
        }

        return $object->getId();
    }

    /**
     * Transforms a value from the transformed representation to its original
     * representation.
     *
     * This method is called when {@link Form::submit()} is called to transform the requests tainted data
     * into an acceptable format for your data processing/model layer.
     *
     * This method must be able to deal with empty values. Usually this will
     * be an empty string, but depending on your implementation other empty
     * values are possible as well (such as empty strings). The reasoning behind
     * this is that value transformers must be chainable. If the
     * reverseTransform() method of the first value transformer outputs an
     * empty string, the second value transformer must be able to process that
     * value.
     *
     * By convention, reverseTransform() should return NULL if an empty string
     * is passed.
     *
     * @param mixed $categoryId The value in the transformed representation
     *
     * @return mixed The value in the original representation
     *
     * @throws TransformationFailedException When the transformation fails.
     */
    public function reverseTransform($id) {

        if (!$id || $id <= 0) {
            return null;
        }

        if(!ctype_digit($id)){
            throw new TransformationFailedException();
        }

        $repo = $this->em->getRepository('...');
        $result = $repo->findOneBy(array('id' => $id));

        if (null === $result) {
            throw new TransformationFailedException(
                sprintf(
                    'Entity with id does not exist!',
                    $id
                )
            );
        }

        return $result;
    }
}

In the IdToMyIntType you would have something like this:

namespace App\YourBundle\Form\Type;

use App\YourBundle\Form\DataTransformer\IdToMyModelTransformer ;
use Doctrine\ORM\EntityManager;
use Symfony\Component\Form\AbstractType;
use Symfony\Component\Form\FormBuilderInterface;
use Symfony\Component\OptionsResolver\OptionsResolverInterface;


class IdToMyModelType extends AbstractType {

    /**
     * @var EntityManager
     */
    private $em;

    /**
     * @param EntityManager $em
     */
    public function __construct( EntityManager $em ) {
        $this->em = $em;
    }

    public function buildForm( FormBuilderInterface $builder, array $options ) {
        $transformer = new IdToMyModelTransformer ( $this->em );
        $builder->addModelTransformer( $transformer );
    }

    public function setDefaultOptions( OptionsResolverInterface $resolver ) {
        $resolver->setDefaults(array('invalid_message' => 'Something went wrong message.'));
    }

    public function getParent() {
        return 'entity';
    }

    public function getName() {
        return 'id_to_model_type';
    }
}

I would suggest you check out the DataTransformerInterface and read the documentation over the methods. It'll briefly explain what is that method expected to do. Also, in case you have problems implementing it, you can always check the official documentation, which contains a working example and build up from there.