It's really hard to give a definitive answer for such a general a situation like that. The results that PT4 displays are based on the hand histories and tournament summaries that were imported, so if you played before you started using PokerTracker then some of your results won't be included.
If you played cash games as well then make sure that you check the cash section as they are separate.
It's also possible that you have played some rebuy tournaments at a site which doesn't inculde rebuy information (or something like that).
Any deposits or withdrawals to the site will not be included in PT4 either.
You could start by checking the data that PT4 has for some individual specific tournaments and see if anything looks wrong. (If it does, attach the hand history and tournament summary files for that tournament(s) to a
Support Ticket so that we can find out why.)