I think they use complicated algorithms to alter ticket prices. Some train companies like Southern and London Midland seem to be more straight forward as they just release cheap tickets around the 12 week date, and then the closer you get to your travel date, as those tickets sell out, the price rises. Other companies operate like some airlines in having flexible prices, so the cheap tickets are released on a drip fed basis at random times within the 12 weeks, and I'm sure the more checking you do on a route, the less likely a cheap seat will be available. I don't know if it's true, but I've been told that some airlines specifically check for IP addresses, and so increase the price if they recognise the same IP address has been checking the same route over the course of a few weeks, and i wouldn't be surprised if some train companies do the same.
