entity_save gives a duplicate entry error even when i specify the primary key

I'm down with a problem for the last one hour. I'm using EntityAPI for my custom entity.

'controller class' => 'EntityAPIController', // and i do not have an EntityClass defined

I'm using the same form for my custom entity add/edit functionality. When the values are submitted from the form, I create an entity array to pass to the entity_save function. While adding, it works like a charm. While editing, in the form submit function, I make sure to have the primary key value to the entity as well. But I get an error that says Duplicate Entry in my base table as it is trying to insert instead of update.

In an attempt to discover the error, I went to entity.controller.inc and found the save function in the controller class. The condition that separates an insert from an update is:

if (!empty($entity->{$this->idKey}) && empty($entity->is_new))

which made me realize that I need to add is_new property as well and set it to false. It still did not work. The problem seems to be with $this->idKey and when I try to see the value of this -- it is empty. The idKey property is not set.

Am I doing something wrong? Or do we need to make sure that idKey is a property of the object too? Please help.