Hi there,
What you are experiencing is caused by internet lag.
http://support.chess.com/Knowledgebase/Article/View/91/0/why-did-the-clock-times-suddenly-change-the-clocks-seem-broken
http://support.chess.com/Knowledgebase/Article/View/121/0/what-is-lag-and-what-are-the-colored-lag-indicators-in-live-chess
I start hating this.. I have lost about 25 games like this! My oponent runs out of time, while I have plenty left. Clock counts down normally until about 15 sec before his time runs out. Then the clock starts adding time to his clock after each of his moves. Eventually I run out of time... What the.... Can someone please help? It's frustrating.. Thanks!!