So now I'm thinking that the cleanbox has some kind of fault... Do people think that's likely?
When faced with faults of this kind one has to apply a logical process to find and eliminate the problem, and that requires technical understanding of all the equipment concerned, it's I/O wiring, the significance of the cable wiring connecting to and from the transformer box, and any environmental factors such as the proximity of strong magnetic radiators like mains transformers.
Fundamentally, when a buzz or other noise is due to a ground loop, breaking the ground loop with a transformer will remove the ground loop noise. But in multichannel systems there are probably multiple ground loops and they will all eed to be dealt with.
Different transformer boxes are wired differently in respect of the case and I/O connector grounds. It is very easy to effectively re-make the ground loop or even create additional loops by using inappropriate balanced/unbalanced cables or adapters, or by allowing the case to touch something that is already earthed.
Transformers are also quite susceptible to radiated magnetic fields, so while inserting a transformer isolation box might break a ground loop, if it is then placed directly over a mains transformer it is likely to capture and inject even more hum!
So yes, it is possible that your Cleanbox 2 is faulty... but there is very little in there to go wrong. It's much more likely to be an issue with the cables or connectors you were using, or where you placed the box.
The other possibility is that the ground loop wasn't where you thought it was, and installing the Cleanbox 2 actually removed the grounding from a class II source device. In this situation it is possible for that device to act like an aerial and pick up all manner of radiated interference!
Technical Editor, Sound On Sound