In theory, no: Virgin don't offer discounts on their own tickets through their website (unlike some other TOCs), unless you're buying
their group advance tickets. That said, different booking engines and interfaces will search for fares differently, meaning that some make it easier to find cheap fares. But that's often down to personal preference.
Oh, and there is
Megabus/Megatrain. They offer some cheaper tickets on a limited number of Virgin services from a limited number of stops, which I think are released about 8 weeks in advance.