I have noticed this on Travelocity as well. How far in advance are you trying to book?
In my case, we aren't leaving until June 25, 2006. When I use the fare finding feature, I usually get prices that are based on current special fares. When I click on the date I want, suddenly the rate jumps. For example, I found a flight from PIT to TPA for $103 RT. When I checked for availability I was told that the fare has changed to $263 RT.
My guess is that the system bases its low fares on current prices, then changes to projected/standard fares in the future.
Others may have better answers...