Lag.
I think that when you submit your move, it also sends a time-stamp along with it. The server is still letting your clock tick away, then it receives your move and the time-stamp, which tells it that you actually sent your move a few seconds earlier, and the server corrects the time.
That or it could be the flux capacitor
I was playing a rated live blitz game today, much superior in time compared to my opponent, that only had 0.7 seconds back.
Suddenly, he has 6 seconds, for no apparent reason. There were an addition time of two seconds for each move, so 6 seconds is just strange. I often experience the timer fails to work correctly. Is there any reason for this bug, has it happened much to any of you?