Bait and switch?
It seems I'm not alone in my conspiracy theorizing. Frommers.com featured an article today about this phenomenon, which the airline industry is explaining away by saying the lower fares are "cached" to enable faster searching. So even though they show up in search results, they might not actually be available. The recommendation: if you see a fare you like, buy it right away, instead of price-comparing elsewhere.
Hmmm... that recommendation seems to lean a bit heavily in favor of the airlines, no? Or maybe I'm just making up another conspiracy theory.