Sounds like a typical frequency clip. Your kick is most likely interfering with your bassline, I suggest that you equalize it, or use another kick.

It might be a latency issue. If you have it set too short, then you get clicks and pops. Are you compressing it, cos maybe it's not compressing that first fraction of the sound file. I had this problem when compressing once, I think becasue the attack was too long and the make up gain high, so it redlined but just for the first kick.

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thanks guys