se non ho fatto troppo casino una cosa di questo tipo dovrebbe andare:
codice:
<?php
// file fpdf_js.php

class PDF_Javascript extends FPDF {

    var $javascript;
    var $n_js;

    function IncludeJS($script) {
        $this->javascript=$script;
    }

    function _putjavascript() {
        $this->_newobj();
        $this->n_js=$this->n;
        $this->_out('<<');
        $this->_out('/Names [(EmbeddedJS) '.($this->n+1).' 0 R ]');
        $this->_out('>>');
        $this->_out('endobj');
        $this->_newobj();
        $this->_out('<<');
        $this->_out('/S /JavaScript');
        $this->_out('/JS '.$this->_textstring($this->javascript));
        $this->_out('>>');
        $this->_out('endobj');
    }

    function _putresources() {
        parent::_putresources();
        if (!empty($this->javascript)) {
            $this->_putjavascript();
        }
    }

    function _putcatalog() {
        parent::_putcatalog();
        if (isset($this->javascript)) {
            $this->_out('/Names <</JavaScript '.($this->n_js).' 0 R>>');
        }
    }
}
?>

<?php 
// file classe_stampa.php

class PDF_classe extends PDF_Javascript 
{ 
	function Row($data) 
	{ 
		$this->SetFillColor(232,232,232); 
		$this->SetFont('Arial','',8); 
		//Numero
		$this->SetY(2); 
		$this->Cell(50,0,'Numero Protocollo',0,0,'L',0); 
		$this->Cell(1,0,$data[Numero],0,0,'R',0); 
		//Data
		$this->SetY(5); 
		$this->Cell(0,0,'Data',0,0,'L',0); 
		$this->Cell(0,0,$data[data_prot],0,0,'R',0); 
		//Cognome
		$this->SetY(8); 
		$this->Cell(0,0,'Cognome',0,0,'L',0); 
		$this->Cell(0,0,$data[Cognome],0,0,'R',0); 

		//Nome
		$this->SetY(11); 
		$this->Cell(0,0,'Nome',0,0,'L',0); 
		$this->Cell(0,0,$data[Nome],0,0,'R',0); 
		//Oggetto
		$this->SetY(14); 
		$this->Cell(0,0,'Oggetto',0,0,'L',0); 
		$this->Cell(0,0,$data[Oggetto],0,0,'R',0); 
	} 

	function Table($query) 
	{ 
	    //errore query
	    $res=mysql_query($query) or die('Error: '.mysql_error()."
Query: $query"); 
		while($row=mysql_fetch_array($res)) 
		{ 
			$this->AddPage(); 
			$this->Row($row); 
			//$this->AddPage();
		} 
	} 
}
?>  



<?php 
define('FPDF_FONTPATH','font/'); 
include ("config.php"); 
require('fpdf/fpdf.php'); 
require('fpdf_js.php');
require('classe_stampa.php'); 

class PDF_AutoPrint extends PDF_classe
{
	function AutoPrint($dialog=false)
	{
    		//Embed some JavaScript to show the print dialog or start printing immediately
		$param=($dialog ? 'true' : 'false');
		$script="print($param);";
		$this->IncludeJS($script);
	}
}

$pdf=new PDF_AutoPrint();
$pdf->AliasNbPages(); 
$pdf->Open(); 
$pdf->Table("SELECT * ,DATE_FORMAT(Data,'%d/%m/%Y') as data_prot FROM protocollo"); 
//Launch the print dialog
$pdf->AutoPrint(true);
$pdf->Output(); 

?>