BurritoHmm. I'd agree that it probably has something to do with the footbeds, since it's the common factor. What's the material on the bottom of those footbeds? If it's moving inside your liner, or even if the liner is alternating between tight and loose against it as you flex the boot, I could see the edge or bottom of the footbed getting kind of stuck on the sides of the liner and squeaking/farting the same way you sometimes do getting on and off a leather couch.
There's foam posting all over the place on the underside. I've got powerwraps, so it shouldn't shift around.
The bubble seems to start under my foot, between the sock and footbed in the arch area, and as I ski around it tries to escape out the heel pocket and up the Achilles. Heel cup and hold are on point so it doesn't make it past there.
It's probably actually always an issue, but I only notice it at the end of the day. By that point my feet are sweaty af, my socks are saturated, and it starts to seal completely around the heel and lower cuff.