Category Attributes, Setup Script and Flat Tables

Each of your custom attributes needs a source model with the following methods defined:

1. getFlatColums(): creates the value column on the flat tables
2. getFlatUpdateSelect(): populates the values

You can also specify an index for this column by defining getFlatIndexes().

For reference see Mage_Eav_Model_Entity_Attribute_Source_Boolean:

/**
 * Retrieve flat column definition
 *
 * @return array
 */
public function getFlatColums()
{
    $attributeCode = $this->getAttribute()->getAttributeCode();
    $column = array(
        'unsigned'  => false,
        'default'   => null,
        'extra'     => null
    );

    if (Mage::helper('core')->useDbCompatibleMode()) {
        $column['type']     = 'tinyint(1)';
        $column['is_null']  = true;
    } else {
        $column['type']     = Varien_Db_Ddl_Table::TYPE_SMALLINT;
        $column['length']   = 1;
        $column['nullable'] = true;
        $column['comment']  = $attributeCode . ' column';
    }

    return array($attributeCode => $column);
}

/**
 * Retrieve Indexes(s) for Flat
 *
 * @return array
 */
public function getFlatIndexes()
{
    $indexes = array();

    $index = 'IDX_' . strtoupper($this->getAttribute()->getAttributeCode());
    $indexes[$index] = array(
        'type'      => 'index',
        'fields'    => array($this->getAttribute()->getAttributeCode())
    );

    return $indexes;
}

/**
 * Retrieve Select For Flat Attribute update
 *
 * @param int $store
 * @return Varien_Db_Select|null
 */
public function getFlatUpdateSelect($store)
{
    return Mage::getResourceModel('eav/entity_attribute')
        ->getFlatUpdateSelect($this->getAttribute(), $store);
}

/**
 * Get a text for index option value
 *
 * @param  string|int $value
 * @return string|bool
 */
public function getIndexOptionText($value)
{
    switch ($value) {
        case self::VALUE_YES:
            return 'Yes';
        case self::VALUE_NO:
            return 'No';
    }

    return parent::getIndexOptionText($value);
}