Post your script string info that you start cgminer with, and how long did you monitor the pools hash on website, sometimes it takes a few minutes (totally random) to start tracking properly and even then its not always an exact to what you see in cgminer but relatively close to it. You have to account for delay and update time and all that.
Let it run for 10mins and then check see what it registers on the site if it still isnt full but going up from that 1khash give it a lil more time it will even out.