Carbon-metallic Brake Pads
If you do have carbon-metallic brake pads, especially high performance ones like you might find on an Audi S4 (although I can't say for sure), the material that they are made out of do tend to be prone to noise which is an artifact that occurs from the manufacturer trying to optimise for braking efficiency.
How to Fix Brake Noise
Here is a quote from a website that you may find useful:
If the noise pops up just before your vehicle comes to a complete stop, as opposed to squealing throughout the entire range of braking, the cause could be a brake pad that is vibrating against the rotor. A set of brake pad vibration damper pads could cure the squeal, but there's no guarantee.
You did say that
it comes and goes, but you also said that for the most part
its always there so I don't know if new brake pad vibration damper pads are going to fix your particular issue but it is definitely something to consider.
Another thing to consider would be to replace your brake pads altogether, which may be expensive and doesn't guarantee that it will fix your issue. Also I suspect that it would void your warranty, which on such a new, heavily depreciating car like yours you probably want to do!
Otherwise, the only thing I can suggest is taking it back to the dealer to see what they say. Especially if it is happening all the time, not just when you come to a stop.
Note: If you have a rather sporty driving style or you go for a track day, your brake temperatures can get hot. It is normal if the brakes produce noise at this point. Just stop and let them cool down for a while.