i hope someone answers your prblm cuz i see the same thing happening in some of my game...the little red square upper right flashes but the time doesnt start for several seconds
time fails to elapse in quick game

i think thats just lag experienced, and your opponent sees the same thing on his/her side. lag is adjusted towards the end of the game, appearing as time bonuses, which REALLY annoys me cuz u cud be up on time throughout most of the game, only to find that in reality u were down on time... but u wouldnt no this till the final 10 or so seconds of the game. i wrote an email to chess.com about this and they said its just an unfortunate part of live chess as it currently is, and they hope to address it in the new version of live chess if and when it comes out.
what im talking about though is when, both players have been making moves, but one players time does not elapse until the mid game, after which things proceed as usual, albeit with one player about 20 seconds up. one other thing; ive only noticed this in quick games, not long or even blitz. however, i have seen the lag thing where the timer stutters and then counts down appears in all live games.

i guess this post is no longer relevent, with the advent of Live Chess 2 making lag all but obselete (assuming both players have good internet connection, that is).
Live Chess 2 really increases the damage one can do with pre-moves, as they cause ZERO time to elapse, which can be devestating for the other player in bullet chess. (i'd no, having been on the recieving end of it)
this occurs very rarely, but i have seen it happen at least 5 or so times out of the 275 quick games i have played. for the first several moves the opponent makes, no time elapses for them, until we are well and truly into the mid game, and only then does time begin to pass for them. im thinking maybe if one uses the pre-move setting this may happen? especially for openings where you pretty much no what ur gonna do. whatever the case, it is a great advantage, as it leaves them 20 some seconds ahead (even with the way i play: i drag my peices to the spot i plan to move them while its the opponents turn, and drop them once the timer indicates its my turn, let alone if i wait for the timer to start before i commence to move my peices)
my internet connection on the bar thing shows full green, or four fifths green at the least, so im very hesitant to put it to poor internet connection. maybe its cuz im all the way down under? just a thought. any answers to this anomaly are appreciated :)
Wu Gambino