I only ever had that problem when I either
1. focus on something other than the game (the flash object), this cause the computer to attempt to save power and "powerdown" flash which causes it to lose sync with server. (usually this is caused by minimizing window or tabbing away, but depending on browser etc, it might happen without those)
2. Have a bad internet connection.
Unless this is a wide spread problem on your server, which might indicate a badly configured server (it's possible), this would be YOUR problem.