Rake is removed from pots you win and if PokerCraft isn't adjusting for that in the graphs they are displaying the information will be blatantly wrong and not a true representation of your actual win/loss (which is what it should be according to the legend in your PokerCraft screenshot). If you want to add attributed rake and attributed jackpot rake to your net results in PokerTracker 4 you can do so with custom statistics. See
this guide for the basics on custom statistics creation and
this guide for a deeper walkthrough. The latter was written for PokerTracker 3 but the techniques all apply to PokerTracker 4, the interface is just slightly different.