[eluser]CroNiX[/eluser]
You're either hitting the php timeout (max_execution_time) value, or the webservers. I believe they default to 300 seconds. So if you send a request to the webserver and it takes longer than that period of time before sending the response back, you get that message.
It has nothing to do specifically with CI, other than whatever you are doing is taking longer than the timeout period allows. Sometimes it's due to an overloaded server, like if you're on a shared host and the other websites are hogging the CPU, so it doesn't process as fast.
