Red is currently working this problem diligently for me, but I thought I would see if anyone else had this problem.
I can use one mic, plugged into the front of the Scarlet, perfect. I can plug the same mic into either side and be fine. I have done this with 2 dynamic mics, same model/specs. If I plug both in I get mixed results, most of the time bad. I get crackling, pops, and drop signal here and there. All this while being well under clipping due to input/volume levels. I thought it was a bad export of the footage, but I did it a few times and got the same audio. And it is in the audio files, its not playback.
I had an audio tech look at the files and since I did many tests with different mics, XLR cables, we were able to rule out a bad mic/cable or L or R side of the camera. I also tested each mic/cable with my Zoom H4n recorder, one, then 2, with perfect results in all situations.
I had these problems dispite being on a few different firmwares, I have had 3.0.0 and 3.2.8 beta.