I've had a quick play-around with the new booking site, and I seem to have stumbled upon something interesting.
As part of a potential journey from my home station Arlesey to Southend Central on March 24th, I did a search for fares from Barking to SOC (I normally use a day travelcard from Arlesey and a return from Upminster to SOC, but engineering works on that day mean all fast C2C services are diverting via Dagenham Dock, so hence splitting at Barking for this). Expecting to see the usual £7.40 fare for a network railcard discounted super off-peak day return, I was quite surprised to see it showing a £6.50 off-peak day return as the cheapest fare for the journey:
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I've checked on National Rail Enquiries, LNER's and VTWC's websites, and all three list the £7.40 super off-peak day return as the cheapest fare.
BRFares also lists the £7.40 as the cheapest return fare for this journey. So it would be interesting to see how the C2C engine has come up with this £6.50 fare.
**EDIT: I think I understand why this is happening. The C2C website says they offer a 'discount' for off-peak fares bought at least 3 days in advance if booked through the C2C website. I'm guessing that is what is applying here, and also explains why NRE/LNER/VTWC aren't showing it. So nothing special with the booking engine.