Importing troubles

No doubt when someone gives me the answer to this I will feel like an idiot, but it won't be the first time, so here goes:
Every time I update a new PT3 beta I re-import my hand histories. In my previous db (PT3.5) I had 406K hand histories, including 11K hands of my own. After reimporting for PT3.5 I have 272K hands, including just 6K hands of my own. I play on Full Tilt exclusively, and when importing I did two separate imports, using "Import from Directory" (with "include sub-directories" checked), one from C:\Program Files\Full Tilt Poker\HandHistory, the other from C:\Program Files\PokerTracker 3\Processed.
The reimport had a ton of duplicates (more than original hand histories) and, as I said, over 130K less hands.
I feel dumb about this, but I'm a first time PT user (used to use Poker Office) and am still figuring out how it works.
Thansk for any help...
Every time I update a new PT3 beta I re-import my hand histories. In my previous db (PT3.5) I had 406K hand histories, including 11K hands of my own. After reimporting for PT3.5 I have 272K hands, including just 6K hands of my own. I play on Full Tilt exclusively, and when importing I did two separate imports, using "Import from Directory" (with "include sub-directories" checked), one from C:\Program Files\Full Tilt Poker\HandHistory, the other from C:\Program Files\PokerTracker 3\Processed.
The reimport had a ton of duplicates (more than original hand histories) and, as I said, over 130K less hands.
I feel dumb about this, but I'm a first time PT user (used to use Poker Office) and am still figuring out how it works.
Thansk for any help...