I still think this is an Apple issue, not Apogee. I mentioned this a few weeks ago, but I have this issue with a new iMac 27" delivered last month, with a Samson USB mic that had worked fine for years. Having tried everything I could think of, I ended up buying a new Shure PG42 USB mic, and I have exactly the same issue from the start. I can record for a few seconds to a few minutes, then boom! The crackling starts and I have to unplug the mic and plug it in again to fix it.
I can use both mics fine on my 1 year old MacBook Pro. I tried re-installing the iMac from scratch. No different.
I have spent a couple of hours on the phone with Apple Support here in Japan where I live, and they spent a few days last week, then reported back on Sunday that they can reproduce the issue. They didn't say which USB mic they were using, but I don't think it makes any difference.
They of course did not commit to a fix or a timeframe, but have recognized that there is an issue and said they would continue to try and find a solution.
As it stands, I can't use either USB mic for recording, Skype, Google Hangouts, nothing. It either goes noisy as crackly, or it crashes my iMac after a while.
One thing I noticed that made it better, was unplugging the electric cord to my Belkin Thunderbolt hub. Just unplugging the Thunderbolt cable from the iMac didn't make a difference, but actually turning it off did.
I don't know if the iMac is succeptable to static or noise from other devices, or if the Belkin hub is even emitting any, but when that is turned off, I can work for much longer without an issue. After about 30 minutes of recording or talking on Skype though, my iMac freezes and I have to reboot. It's fine otherwise. It only freezes when I'm using the mic. Very frustrating.