I was receiving this message last night, and in fact it removed me from the game back to the char selection screen. I was under the impression that it was due to the stress load of players on the hardware.
I been having the same problem for days..
I keep getting "Server not responding" error and then get disconnected constantly in populated areas. seems fine when I'm on my own in an instance, IF i can make it that far, and even then sometimes i get the msg. it's really annoying as i can't get a decent game session in, and often not even enough time to send in a bug report cos i get disconnected.
lots of other ppl having the same problem check out http://forums.startrekonline.com/showthread.php?t=59403