Here's what's up... The stereo "pairing" between say, two Flip 6s using "Partyboost", happens between the speakers (two channel stereo). In other words, music is sent to a speaker, and the firmware of that speaker determines which channel it plays and which channel is sent to its partner speaker (both channels are not the same).
Having both speakers paired up in Bluetooth settings sends the same data to each speaker, each of which attempts to do its part by playing one channel and sending the other to its partner speaker... And the result is a choppy, horrible sounding mish-mash of the two. The speakers were not designed to receive and process the same data... One is the pitcher, and the other is the catcher, so to speak. It doesn't matter which one is which as long as one speaker pitches and one speaker catches.
The solution is to "forget" one of the speakers in your Bluetooth settings, and allow the firmware of your speakers to perform the separation and playing of stereo channels, by using the specialized buttons on whatever speakers you're using to connect to each other. Those buttons are essentially telling one speaker it's the pitcher, and the other is the catcher. The app does the same thing.
Where JBL has dropped the ball is in the implementation of the firmware. It should prevent BOTH Bluetooth speakers from performing the same role but instead seems to encourage it, making it impossible for what would be otherwise impressive software to do what it was designed to do.
Hope this helps, because once you get through it, the sound quality and performance of these speakers in stereo is nothing short of amazing.