Whenever a device includes a hard drive, a cooling fan or a transformer there's always a chance that there will be some mechanical noise.
Switch-mode power supplies have replaced large transformers in most electronics now, but they still use filter coils (inductors) which are a form of electro-magnet. The thing that the wire s coiled around is called the core. Sometimes they crack and so vibrate.
Inside your Tivo box you have a hard drive, a fan and inductors. Any one of those can be a source of noise. You also have the surface on which the box sits. If the shelf is glass and it's loose on its fixing points then you can get some noise from that too.
Rule out the obvious stuff first. Check it's not the shelf vibrating in loose fixings or something other than the box that could be vibrating in sympathy. Also check that you aren't being hyper sensitive to any small amount of vibration that can't be heard from more than a couple of feet away. Once you have done that and if you are convinced that there is a genuine problem then get in contact with Virgin. The box is always their property, so that means it's always their responsibility too. Get them to send an engineer.