Right... I spoke to a very nice senior manager in the second line support team about this. He said that Virgin are now aware of the issue, however at the time of speaking there is no reference number available to refer to when calling them (this may have changed between then and now).
Basically, as we guessed, it is a problem with a Virgin system, and every V6 (and possibly TiVo box) activated today has been afflicted by this error. He said that from their end, my V6 box was showing up as activated, and was accessible via their systems (as it should be). Their network team are working on it; his advice was to reboot the box every hour to see if they've fixed it. :/
I'm also having this very frustrating issue. The engineer left me with the same error on screen telling me I would receive a call from Virgin within 2 hours to verify the box, and if I didn't to call him on his mobile. After 2 hours I had had no call, so I called the engineer on his mobile as he instructed, left messages etc and he never picked up or called back. I called Virgin, followed all the prompts and as always happens after going through the rigmarole of giving them my details I was told that the system had put me through to the wrong department.
Finally discovered that the correct department to speak to is called the 'LIGHTNING FMC TEAM'. However, they still haven't solved the problem.
I am going to be asking for a refund of 1 day of my monthly payment as they have not been providing the service I am paying for. I suggest that everyone else with the same issue do the same, and perhaps they will learn to communicate problems with their paying customers a little better in the future.