Exactly! The sensation is painful, and sometimes it can be nauseating. Lowering either front window (or locking the rear from being lowered) is the only solution it seems.
I discovered this annoying characteristic with the '06 Odyssey after trading in an '05. A feature of the '05 is the tilt-out rear windows which provide air flow through the van. I did not notice the thumping in the previous model--it is possibly opening the rear windows was the reason.
Honda issued a TSB against the '06 Odyssey regarding a high-pitched whistle heard from the front of the van at highway speeds (a correction kit is available and owners can contact a dealership to have this problem fixed under warranty). I am curious if Honda has issued a TSB regarding the thumping phenomenon--a.k.a., aeolian oscillation; "pop bottle effect"; etc--common to the '06 Odyssey model.
Tim.