I've wondered a lot of it's some kind of phasing issue with monitors vs PA or something to that effect.
This is possible, but I would start with the guitar(s), keyboard and drums, looking for specific tuning conflicts or distortion effects. I worked with a guitar player who tried out a pedal that put out a semblance of Leslie effect, and it totally messed with my ears until it accidentally flew out a second-story window one night.
