That happened to me the other day. I was handily beating a higher-rated player, but because I had a poor Internet connection, each move started taking some time to submit even after I made the move. Flagging is not fun when you're up a rook :( Horribly traumatizing experience.
If you have been having some connection issues, that could be your problem. I just stay away from live chess when my connection misbehaves. Hope this helps.
We are pretty much 3rd world over here, but corruption, tender fraud and internet work perfectly. I don't think connection is the issue. Any other possible cause ??
You weren't playing with an incremental TL by any slim chance? I just played 2 blitz tnmts last nite (5/0 TL) and the clocks seemed OK, although this info may not be much consolation for you. If the problem occurs constantly contact the staff directly via Help & Support, and maybe something in my blog will improve your connection if only slightly http://blog.chess.com/NimzoRoy/diagnosing-and-fixing-internet-problems
I have played several 5 minutes blitz games recently and all of a suden see that my clock is running out with, literally, seconds to go where I see that my opponent is still proudly sitting on 4:14 minutes, although we spent similar time on moves. Where did his sudden 4 minute gain come from ?