It sounds like PokerStars is not saving tournament summary/history files and/or HM3 is not auto importing the summary files. If the summary files are were not being auto imported then you are going to have to request a playing history audit file from the PokerStars Tools menu to review then manually edit the Tournaments report with the right click - 'Edit' option.
Try creating a new folder on your computer such as C:\StarsHands and C:\StarsTourneys then setup PokerStars
to save both the hands/results in their Settings - Playing History - Hand History and Tournament Summary menu and
setup HM3 to Auto Import from there in the Tools - Site Settings - Auto Import Folders menu. Make sure you 'Remove' all the unused auto import folders for the site's default hand history path.
If you continue to have problems: Please zip and email the original problem hand histories and tournament summaries to us as instructed
at the bottom of this FAQ. Make sure you also include screenshots of your reports/filters and a detailed description by tournament number, session, hole cards, filter, stat, etc. of some of the errors we need to test.