To save file in DB, you need to write custom code with on_insert OR on_update event handlers.
For e.g.

// use events if you need custom logic for upload
$e["on_insert"] = array("add_invoice", null, true);
$g->set_events($e);

// callback for add
function add_invoice($data)
{
$upload_file_path = $data["params"]["note"];
// …
}

This callback contains the filename with path, that is uploaded. You can read it's content using file_get_contents and execute a SQL to save in database.

In CI, the querystring are removed by default to make user friendly urls. That may be causing the issue.
try appending QSA in htaccess, when it sends requests to index.php. There may be other cases, but you need to debug using firebug & print_r($_POST); inside code.

would you like to send me an example code?

Hello,

I'm sorry but the code is not there for file uploading in database.
You can refer editing/file-upload.php. It contains event handlers placeholders for your custom code.