For at least the second time now, I have experienced a dropped move in the new interface. This is when my opponent has made a move but it hasn't shown up on my screen.
 
When this happens, I have to reload and then go back into the game to get my board up to date. (This assumes that the Caissa server has registered the move and it got lost on the way to my machine; I don't know if it also sometimes happens that the player has sent the move but Caissa hasn't registered it.)
 
But by the time a minute or three of inactivity prompts a swap of messages to determine that a move has been lost, quite a bit of time has gone from my clock. In the game I just played against otyeko, I had about eight minutes left before the dropped move; when I came back I had only one minute.
 
My guess is that a momentary outage in one's Internet connection at the wrong time can cause this. But whatever the cause, it could be dealt with if the client, in addition to waiting for the server to send a move, could poll the server at intervals to check that the board is up to date. (How long this interval should be would depend on finding the right balance between improving the reliability and not putting too much load on the server.)

If this happens again, check the connection status settings on the main menu. In the upper right of the main menu (behind the game playing window) there is a Connection Status and Lag time. If you think you are disconnected, confirm what these settings are showing. You may have to drag the game playing windows down and to the left for the connection settings to show up.