I've noticed a similar behavior with my vehicle, albeit the travel isn't as much as you're describing. Mine seems to coincide with the A/C shutting off. My guess is a slight change in available vacuum as the compressor dissengages, increasing the amount of vacuum assist slightly. Haven't noticed it much recently, so I'm not too worried about it.
One test I've done before to track down potential master cylinder issues is to pump the brakes with the car off (to get rid of any vacuum) and then hold down the brake pedal with moderate to heavy force. If the pedal doesn't change after 30 seconds or so, then that's a decent indication of solid MC internals. I was able to diagnose a bad piston seal in my Jeep's rear circuit using this method, as the pedal moved towards the floor after 15 seconds or so of holding the pedal.
Obviously, this is not definative by any means, but if no other leaks are found in the system, it may help to rule things out (or identify them). As stated, don't mess around and take chances with your brake system.
Last edited by ras06LGT; 07-10-2013 at 02:31 PM..