entity_load not fetching the updated column
If I have understood you correctly, as well as updating the table you must provide an updated schema definition for the entity. Drupal uses this definition to determine the names and properties of the columns in the entity.

Note you do not need to do an 'update' action for the schema definition: just change it to match the current code. You (only) need the update hook for databases that enabled the earlier version of the module. Also, importantly, the update hook must both add the column to the database, but set the new property value for any rows appropriately. Often this can be done by the database default value, but not always.