I think fares are loaded 3x per day, if I remember an interview from a few years ago.
But I think what you are likely experiencing is a fare bucket selling out, or the time limit for advance purchase passing, not the fare itself changing.
They can be changed 3 times a day. I'm not sure all airlines actually do it 3X a day, but that is what they are allowed via the various ticketing systems. On their own systems (website) I'm not sure, but I doubt they would have seperate procedures for their own website vs. Kayak.
As TA said, it is far more likely that a fare bucket sold out, rather than the airline actually changed a fare.