Could be something internally electronic, too.
I returned an ECM8000 (big surprise, huh?) because of pops and cracks.
Check out weird sources, too. It took me six months to find out what kept making clicking noises come out of my amp when I was at band practice...it turns out there was an electric fence plugged in somewhere in the garage (which happened to be on the same circuit as the practice space).
Other than that, it might be as simple as digital distortion. That can get really ugly. Maybe you could try just pulling your levels down a bit, especially if you're doing digital 24-bit recording...you'd have plenty of headroom, anyway.
