Sean, I had the same problem. Then I realized I had not updated 'checkout_process.php' during the affiliate installation.
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In checkout_process.php in the catalog directory find line
// load the after_process function from the payment modules
$payment_modules->after_process();
and insert before it
// Include OSC-AFFILIATE
require(DIR_WS_INCLUDES . 'affiliate_checkout_process.php');
Good Luck!