Happens to me too from time to time. I usually just hold one fare in a browser (Safari) then open another browser (Firefox) and look up the same fare. Usually one of them will show the lower fare so that's the one I book.

For some reason this doesn't work when opening a second tab within the same browser. I need 2 different browsers. One time in fact, I got really wild and opened Safari and Firefox in Mac OS, then IE in Windows emulation mode on my Mac. Funny enough the IE Windows session had the low fare so that's what I booked.

I don't claim to understand nor do I ask why. I simply book the low fare any way I can.