2004 Honda Pilot Brake Problems?

What's likely happening here is the amount of boost is changing suddenly to make the pedal easier to press. This boost is powered by engine vacuum. One of the following may possibly be happening, or it could be something else entirely: When the transmission is cold, it might downshift suddenly while you are decelerating, increasing the engine speed while the throttle plate is closed, which increases boost. However, this is very unlikely. Another option could be a defective brake booster which has a problem that fixes itself at temperature. I don't claim to be an expert on the inner workings of a brake booster so that's all the info I can provide.