[mistwang]

You need to increase the "Initial request Timeout" to at least the time that the slowest script takes. "Connection Timeout" should be longer than the "Initial request timeout". And the slow script should be made faster if possible. :-)

Would it possibly be better to get rid of the PHP_LSAPI_CHILDREN setting, and set Instances = 100?

yes, it probably do better when instances = 100 in your case, as php processes is directly managed by lshttpd, and whenever a request timed out, the PHP process handling the request will be terminated. Only drawback with this way, PHP processes can not share their opcode cache with each other, not a big deal in most cases.