The sound problem was the mix.
Johnny B. was nowhere to be heard. At least, I didn't hear him in the mix at all during the broadcast. I think, when Chris couldn't hear the guitar, he felt uncomfortable with that empty space that shouldn't have been there. I'm not positive about this, but I watched the clip at MTV.com and they had recut the performance from their footage. It was different than the live broadcast. And, the audio mix was changed as well. There definitly was a weird air to that scene.