I don't think it's the Aegir. I tried multiple combinations of preamps into Aegir and they all worked flawlessly. Also tried different amps with the Freya N, and the popping was still present. Here's a video clip I recorded of the popping...
That definitely is not the way it should be. Send it back to schiit. I don't get that noise. Mine is just static pops which I think is just the design. I don't even use a Schiit amp.