If you use the old echo-inc payment method (which works well for us in 1.3.7), there is an error which scrambles any charge amount over $1000 in this file:

includes/modules/payment/echo_cc.php

See line 268:

Change this:

$echoPHP->set_grand_total(number_format($order->info['total'], 2));

To this:

$echoPHP->set_grand_total(number_format($order->info['total'], 2, '.', ''));

hth