After you play your move, I'm guessing on your screen your opponent's clock starts ticking down. While your move travles through the internet though, your opponent may not have seen it yet due to lag. When he sees your move, his clock starts ticking down (and will be different from his clock on your screen). After he makes his move it comes with a time stamp and when both of these arrive at your computer his clock is adjusted so that only the real time he actually used to contemplate his move is taken off. Because his clock on your screen started before he saw your move, this means time is added.
This info, but in more detail/easier to understand, should be in the FAQ section.
Many times I have been playing and run my oppenents clock out. All the sudden up to 4.5 seconds reappears on their clock. Anyone have this problem? Also I find mt PC slower in the morning and the late afternoon. causes me to loose games by 15 seconds when I never quite moving and in fact was ahead od the clock. Anyone know why? Nancy