The issue is in the AdminOrdersController.php line 440. The test returns false for some reason I cannot figure out.
I forced the condition to true and tracking is now being sent.
if(@Mail::Send((int)$order->id_lang, 'in_transit', Mail::l('Package in transit', (int)$order->id_lang), $templateVars,
$customer->email, $customer->firstname.' '.$customer->lastname, null, null, null, null,
_PS_MAIL_DIR_, true, (int)$order->id_shop))