PokerTracker

I just brought across some FT hands from FT. The import status says that the correct amount of hands were imported , but on the General Tab with no filters set, there are 5 hands missing.

From PT3 import page:
Import complete. 1,736 hands in 7 files were imported. (0 errors, 0 duplicates)

Only 1731 hands are showing up on the general tab.

It did the same for another limit as well. It missed 6 hands after saying all imported successfully.

Yes, I've reported this too.
For me, the missing hands were ones where the hand histories did not include my hold cards. PT2 includes these as hands played, but PT3 does not. (Correct me if I'm wrong..)
If one or more of your 'missing' hands DO include hole cards, I'm sure support would be interested in the HH.

It's likely you had a few observed hands in there that didn't include you at the table.