I'm thinking it might be related to that now that you mention it. The cleanest wave I've ever had was in a nice secluded cove but it was kind of small so you could only go so far before having to turn around. Everywhere else we are usually on big water so it's not the smoothest. You can hear and see the boat rock so perhaps that is the issue. We don't have the luxury of hitting the lakes early or late in the day unfortunately and this year there has been so much boat traffic i'm guessing due to covid and all the boat sales. about 3-4x more boats than in years past.
I bet that is the issue if your hear a change in exhaust noise also. Mine does the same thing when the boat rocks from a wave.
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2018 Moomba Craz
6.2L Raptor 400
6 Pump Ballast, Autowake 2.0, Flow 2.0 Surf System
OJ 15x13 Wake Prop
Digital Cruise Pro 3 (paddle wheel)
Wetsounds Rev 10's