This is a bit more efficient
<?php
$count = count($checkbox);
for ($i=0;$i<$count;$i++) {
# Prepare fonts
$f1 = $pdf->SetFont('Courier');
# Draw Invoice Box
$pdf->Cell(50,8,'INVOICE NUMBER',1);
$pdf->LN();
$pdf->Cell(50,8,$checkbox[$i],1);
$pdf->AddPage();
} //end for
$pdf->Output();
?>
This gains in efficiency because you're not executing an if statement everytime through the loop.
NOTE: If the blank page comes back just change $i<$count to $i<($count-1)