By default the 9.3 server returns maximum 500 records. My guess is you have a lot more features than that, so there's a bunch of them you don't see, because the server never returns them. Try and set the Mode on the FeatureLayer to OnDemand, and it should only request the features in the current view. If you pan it will progressively get more and more features. As long as you never have more than 500 records in the current map view, you shoulnd't be seeing any missing features.