The bubble that I had appeared several hours after I set it up, which meant it was as it came to room temp.
When I cut it, I saw that the frosting had separated from the cake...so the air bubble was between the cake and the frosting, NOT between the fondant and the frosting. I think maybe it must somehow come from between the layers.
I also do alot of refrigeration. I think the refrigeration helps keep from getting the middle "bulge" because if everything is firmed up all the way through the cake before adding fondant, then the pressure you are using to smooth the fondant will not cause the cake to settle and bulge the frosting out the sides.
As far as the bubbles...its scary! But I just try to make sure I am not leaving gaps when I spread my buttercream...and also alot of times I use wire/stars and whatever, and I bet on those cakes, or any cake you actually stick something in, helps avoid bubbles. Not sure the answer though...really....