TCP window size

I am using Iperf V 1.7.0 on Redhat Linux 9. I have set up one TCP connection with a specified received TCP window size. I captured the received sequence of packet using ethereal and use some scripts to calculate the approx. TCP window size variation for the duration of an experiment. What the script does is to calculate the amount of data transmitting during the roundtrip delay which should represent the outstanding data in the link from the time the packet was sent until the time of ack. arrival. However, the approx. TCP window size never reaches the TCP window size value I have specified in Iperf. Even the specified TCP window size value is very small (such as 5 kbytes with the packet size of 648 bytes), it will never reach that value. Also when the packet size is changed, the larger packet size always reach higher TCP window size. I don't understand why this is the case since we specified the TCP window size in the unit of Kbytes not packet.