Existing taxonomy terms not being assigned to domains

When enabling taxonomy terms, existing terms are not being correctly assigned to domains and become invisible until you disable the access again.

The cause is:

$query->fieldCondition($field_name, 'domain_id', NULL);

Which is making the EntityFieldQuery return no results and therefore the $unaffiliated_entries array is empty.

A quick fix is to comment out this line (735 of domain_entity.module)