Schiit uses different clocks for 44.1K vs 48K (and multiples thereof for 88.2K and 96K, etc.) This gives the most precise handling of the digital to analog conversion. Cheaper DACs will use a single clock and approximate the sample frequency. Schiit uses relays to switch clocks, hence the noise you hear. Sounds like the short delay between the left and right is that the relay on one channel is switching faster than its brother on the other channel.
I'd suggest you email Schiit and ask them if this is something that can be addressed. Might be a component in one channel is a bit off-spec.