Magento – Product position in top level category not working

You need to rewrite the method Mage_Catalog_Model_Resource_Product::_saveCategories
Somewhere in there this is this:

$data[] = array(
    'category_id' => (int)$categoryId,
    'product_id'  => (int)$object->getId(),
    'position'    => 1
);

Replace 1 with 100.
To rewrite the resource model add this to the config.xml of your custom module inside the global tag

<models>
    <catalog_resource>
        <rewrite>
            <product>[Namespace]_[Module]_Model_Resource_Product</product>
        </rewrite>
    </catalog_resource>
</models>

Then create the class [Namespace]_[Module]_Model_Resource_Product that extends Mage_Catalog_Model_Resource_Product, copy the method _saveCategories to it and replace 1 with 100.

There is no method or event to change this. If you want to change default value you can rewrite Mage_Catalog_Model_Resource_Category::_saveCategoryProducts

/**
 * Add products to category
 */
if (!empty($insert)) {
    $data = array();
    foreach ($insert as $productId => $position) {
        $data[] = array(
            'category_id' => (int)$id,
            'product_id'  => (int)$productId,
            // changed code
            // 'position'    => (int)$position
            'position'    => (int)$position ? (int)$position : 100
        );
    }
    $adapter->insertMultiple($this->_categoryProductTable, $data);
}

This should set position to 100 if you do not enter a value.