[Bumping from fall 2014 to be helpful.] I wanted to use the Spanish RENFE website to get the deep-discount PROMO fares. The RENFE website can be frustrating, inconsistent, and has a bad reputation out there on blogs, BUT you can be successful. Trust me. There are great tutorials on Seat 61, TripAdvisor, Rick's websites/books/forums, among others, which tell you exactly the step-by-step process, what the Spanish terms mean, etc...
After reading everything out there, and spending a frustrating hour trying and trying myself, my conclusions are in order to use the RENFE website to get the deep-discounted Promo fares (if booking early enough), you need to use a credit or debit card that has a Verified by Visa (VBV) password associated with it. My regular airline-branded Chase card does not use VBV (Chase does not use VBV), and THAT is why it would not work and I kept getting error messages popping up at the end of the transaction. Once I switched to trying my bank-branded Visa Debit card I was automatically prompted to subscribe to VBV during the purchase process. Once I established the password, I logged back out (to reset the website), and tried the purchase again. The website then asked for my VBV password and the transaction went through perfectly the first time.
As far as the difference between the RENFE Spanish website, and the American portal to it, Petrabax, I could not find any direct cost comparisons or anywhere that indicated the % markup that Petrabax adds onto the standard RENFE prices. So I did the comparison myself.
My wife and I are taking three train trips while in Spain. All three trips were purchased almost three months in advance of the travel dates. All prices shown are discounted Promo fares in Turista Class (Second Class), which were available when I booked.
For Barcelona - Madrid (AVE 2 hrs 45 min)
Purchase via Renfe: €57.60 ea x 2 = €115.20 or about $154.72 USD
Purchase via Petrabax: $98.00 ea x 2 = $196.00 USD
For Madrid - Granada (Altaria 4 hrs 30 min)
Purchase via Renfe: €41.05 ea x 2 = €82.10 or about $110.27 USD
Purchase via Petrabax: $70.00 ea x 2 = $140.00 USD
For Sevilla - Barcelona (AVE 5 hrs 30 min)
Purchase via Renfe: €69.95 ea x 2 = €$139.90 or about $187.90 USD
Purchase via Petrabax: $119.00 ea x 2 = $238.00 USD
SAVINGS RECAP:
Total via Renfe: $452.89 USD
Total via Petrabax: $574.00 USD
Total Savings using Renfe for the three trips vs using Petrabax = $121.11 USD
So, to me, it was worth using the RENFE Spanish website to save the $.
I have also been looking into the differences between Verified by Visa and Visa Checkout. At this time it appears these are two independent third party verification programs. Banks or credit card issuers can elect to use one of these different programs for their credit or debit cards, according to the person I spoke with. My direct inquires to Visa Checkout advised that I needed to contact Verified by Visa directly for information or questions about that program: "Thank you for contacting Visa Checkout customer support. Your email has been misrouted to Visa Checkout, and we are not able to respond to your request regarding Verified by Visa. Visa Checkout is a payment service from Visa launched in 2012. With a Visa Checkout account, you can easily make online payments with Visa and other major card brands through one service...
We suggest you contact your financial institution and ask to speak with a Verified by Visa customer service agent to further assist you on your inquiry."