I'm not sure if any one is still running into this problem but I just recently had a problem like this when installing PDF invoice myself. The solution I found for it was to add a strip_tags call on the order totals.
Look for this line:
$pdf->MultiCell(100,6,$order->totals[$i]['title'] . ' ' . $order->totals[$i]['text'],0,'R');
and make it this:
$pdf->MultiCell(100,6,strip_tags($order->totals[$i]['title']) . ' ' . strip_tags($order->totals[$i]['text']),0,'R');
This exact line may not exist in your version of the invoice file if you have changed the location of the totals and such (the 100 and 6 are probably different). Just look for a line similar to this. It should be just above the original comment that says "Draw the shipping address for label."
Hope this helps someone!