Unexpected Entity Reference Autocomplete behaviour
I think you might have not specified the "label" column in the entity definition. That goes within the 'entity keys' array, like the 'id' key.

$entity_info = array(
   .....
  'entity keys' array(
    'id' =&gt; 'primary key column...',
    'label' =&gt;  'column holding the label'
  ),
)


Otherwise entityreference will not know which column to use for searching in the DB. That still makes it possible to show the label  (as you're experiencing) after you reference the entity, because 'label' key is not mandatory, and you may have specified a "label callback" instead, which the Entity API will use when entity_label() is called to get the label of a specific entity.

If adding the 'label' column and flushing all caches doesn't solve your problem, I think I'd need the entity definition to be able to help!