I have found a similar situation, manual submission seems to do better than automatic. Having spoken to may like minded promoters, it seems that (especially infoseek) if you check the state of your newly submitted url too quickly (the auto software does it almost immediately) you get a penalised. I added a url via a tools two days ago. I then added a similar page manually. Currently the tools submitted page has yet to be indexed. Draw your own conclusions.
I have found that AltaVista works the same either method.