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The increment_id column need to have the additional

'filter_index'=>'main_table.increment_id',

Copy file

app/code/core/Mage/Adminhtml/Block/Sales/Order/Grid.php 

to

app/code/local/Mage/Adminhtml/Block/Sales/Order/Grid.php

Find function _prepareColumns()

Change

   $this->addColumn('real_order_id', array(
        'header'=> Mage::helper('sales')->__('Order #'),
        'width' => '80px',
        'type'  => 'text',
        'index' => 'increment_id',
    ));

To

   $this->addColumn('real_order_id', array(
        'header'=> Mage::helper('sales')->__('Order #'),
        'width' => '80px',
        'type'  => 'text',
        'index' => 'increment_id',
        'filter_index'=>'main_table.increment_id',
    ));