Hi Jason,
I have the same problem with Payflow Pro.
The taxes for the shipping costs are the only amount not going thru.
The oscommerce invoice indicates the correct total but the gateway and credit card transaction shows less.
I have previously asked on this forum but no answer yet. I also inquired directly at the Payflow gateway forum and they think it may be an incorrect code in the AMT field.
I looked in the paypal_payflow_pro.php file for this code but not sure if the code is right or wrong.
'FREIGHTAMT' => round($order->info['shipping_cost'], 2),
'TAXAMT' => round($order->info['tax'], 2),
'AMT' => round($order->info['total'], 2),
Unfortunately I am not familiar with this payment module so I'm lost.
I hope someone more knowledgeable with this module can point us in the right direction.
If I find something I'll post it here.