Small thing: In the BOOM setup menu under Wireless Headsets, have you tried disabling and then enabling the Rider Headset? It basically refreshes the pairing between the headset and your WHIM. It's usually the first thing I try if my headset lacks audio.

Personally I don't like to have Bluetooth turned on in my phone when I'm using the Sena headsets and WHIM. My phone is always plugged into the USB port connector. I try to eliminate pathways that I don't want the bike-phone-headset to establish. I want my headset able to pair only to the bike (WHIM) and not my phone. Phone is connected via cable with Bluetooth off.

I agree with the idea that this issue is likely more bike-related than headset. If that proves true, (and you've run through every possible remedy in settings) then it distills down to a software issue in all likelihood. In that case the likely route would be an update and dealer-flash of the bike's audio/WHIM.

 

I originally fixed this problem by using my corded headset and removing the WHIM from the bike. Some time ago I watched "Law Abiding Bike video" that seemed to have a very similar problem and the fix was to go back to the previous WHIM firmware version. I did that and the WHIM and my Sena20EVO headset worked again with the Boom Box. Since then I have come to realize that music from my phone sounds better when paired directly to my headset rather than go thru the Boom Box. I have the HD speakers from Sena and now use my phone for all music and navigation.