normal files transfer speed as compared to iperf speed as measured

I am actually doing some speed test.
I am monitoring my network throughput using netperc while doing a normal copy and paste file transfer over a network connection and the speed I am getting is not up to my mark from the netperc monitoring output BUT when I am using an Iperf or Jperf to do further diagnosis the throughput is up to what I am expecting. What is the difference between a normal file transfer for eg using 3cdaemon as compared to iperf?Network issue or? Any advise appreciated.