Add payment method to transaction so that users see 'Paypal WPS' instead of 'Unknown' in the Order UI

Hmm, I'm curious as to why this is necessary. The following code should initialize this to the proper value:

  // Create a new payment transaction for the order.
  $transaction = commerce_payment_transaction_new('paypal_wps', $order->order_id);
  $transaction->instance_id = $payment_method['instance_id'];

Hmm, it's explicitly setting payment_method if you look at the commerce_payment_transaction_new() function:

function commerce_payment_transaction_new($method_id = '', $order_id = 0) {
  return entity_get_controller('commerce_payment_transaction')->create(array(
    'payment_method' => $method_id,
    'order_id' => $order_id,
  ));
}

I don't suppose you have anything else interacting w/ newly created transactions?

Ok, great.

In case others run into this, I had a problem with a dev site being protected by htaccess/htpasswd. Disabling the htaccess password temporarily while I test e-commerce stuff fixed this for me.