I'm not sure if this is only in v5, but we have upgraded to v5. I don't know if the problem was there in versions before. We realized Google Checkout fees were not being recorded in the WHMCS transactions. Also, if 2Checkout cancels an order / refunds automatically, it does not get recorded in WHMCS either. 2Checkout may cancel an order for fraud and automatically refund the client, but WHMCS does not get notified of this, and we have to manually check to see if the order was refunded or cancelled. This problem also occurs with Google Checkout.
Anyone having these problems too?