Pulsation/Squeak

Hi. My 2001 Honda Civic LX with 95,000 miles on it makes a low pitched squeaking rhythm when I break and come to a stop. This doesn't happen all the time, I notice after i've been driving for 30 minutes or more it starts to do this when I come to a slow. I took it to the dealer to have them check it out and they said they heard it but could not pin point where it was coming from. They said all the breaks/joints looked great and were only at 30% wear. Should I worry about this? My car has only been driven 1500 miles in the last year could it be a joint needs to be lubed up or has become dull? If so, why would this only happen after 30 minutes or more of driving?