I manually imported all of my hands in 2008 from the original hand history files and compared the results in PT2 and PT2.
The only discrepancy I've found so far is one hand from a heads up tournament which appears to load to the database, but does not show up anywhere in the tallies.
When importing , PT3 says 2,402 hands were imported. The "General", "Hands", and "Position" tabs all show 2,401 hands. I located the missing hand and it is a special case - it was the last hand of a heads-up tournament where the other player was sitting out and got blinded out.
I tried to reload that hand history individually, and it appears as a duplicate, so it seems the hand is in the database somewhere, just not showing up.
Below is the hand history in question. Everything I've experimented with so far looks great. Good job.
POKERSTARS GAME #14495000835: TOURNAMENT #73520354, $110+$5 HOLD'EM NO LIMIT - MATCH ROUND I, LEVEL V (75/150) - 2008/01/12 - 00:23:40 (ET)
Table '73520354 1' 2-max Seat #2 is the button
Seat 1: FloppedFlush (2925 in chips)
Seat 2: jcharette08 (75 in chips) is sitting out
jcharette08: posts small blind 75 and is all-in
FloppedFlush: posts big blind 150
*** HOLE CARDS ***
Dealt to FloppedFlush [Td 8c]
jcharette08: folds
jcharette08 has returned
FloppedFlush collected 150 from pot
*** SUMMARY ***
Total pot 150 | Rake 0
Seat 1: FloppedFlush (big blind) collected (150)
Seat 2: jcharette08 (button) (small blind) folded before Flop