I am not aware of a specific issue and you haven't included any relevant details about your problem but bear in mind the following:
1. Rake wasn't supported initially as GGPoker didn't provide those details in the hand histories. GGPoker rake is supported now in PokerTracker 4 so make sure you are using the
latest version but that doesn't fix hands that were imported earlier - those would need to be purged and reimported.
2. PokerTracker 4 doesn't support hands that are run more than twice.
3. If your are referring to all-in equity adjusted results PokerCraft does not use the exact same calculations as PokerTracker 4.
4. If you are referring to tournaments then you may need to
update tournament information manually since as far as I am aware GGPoker to not include full tournament summary information in their files.
5. 6+ Holdem games are not supported.