For now, our Engineering Team is actively working with PayPal to determine why fees aren't bringing into QuickBooks. We are still investigating this unexpected behavior.
We are all hands on deck up and running together for an immediate fix to sort everything out. While they do, I would advise you to get in touch with our QuickBooks Support and have them attach your case to the investigation, so they can add your account information to the notification list. Any progress will be communicated via email.