For me at least for quite some time now. account - bcyber I have several keywords ranking between #1-10 but don't show up on the keyword tracker.
the tracker works mosta ccurately when you jjust use the domain name. eg. instead of www.domain.com use simply domain.com. this produces the most accurate results. I havent had any problems since I began doing this.
I have had yahoo results not sure correctly when A search term was at #1 because of a yahoo tracking url. After a couple of weeks they removed the tracking URL and all showed correclty on the KW tracker.