Sounds like a bad cable on-stage. Since you patched the board, and it sounds really faint, it was probably a bad wire to one of the monitors, and the crackling sound bled through to one of the mics.
Here's a trick to removing random little noise like that when using Waves X-Noise... take a noise-print (Learn) off the unaffected audio of that song by letting the noise-reduction tool learn as much as possible over a similar sounding part of the song. Then highlight the noisy part and process the noise-reduction plugin over the bad part--but set it in Difference mode. The "good" audio should filter through, while the crackling is suppressed.