If you miss your turn due to the timeout do your cities still produce units?
I have a game where my opponent appears to have missed a few turns and I don't see any production in his cities when I go again. So either I mis-remember the number of units he has (seems unlikely as it's early in the game and he has <20 units) or he isn't getting any production on lost turns or he isn't producing anything.
I don't think missing your turn should cost you production as you already pay a harsh penalty for the missed turn.
KGB