PokerTracker

On some of my hands that have imported into PT4, it is showing that I have won/lost an enormous amount of BB in a hand.

For a hand where the blinds were 4000/8000, ante 600, I lost 81k chips but it is showing as losing -10,000BB. They all seem to be from iPoker.

Is this a known problem and is there a way to resolve it?

That should be fixed in the next release. You can download a pre-release version from here but to fix hands already imported you will need to purge the affected tournament(s) and then reimport them.