Flywalker
I seem to have fixed the issue on my end, not entirely sure what caused it. But deleting the affected apps, reboot and then reinstalling them from the google play store fixed the issue for me.
I think it may have something to do with the way Araura store handles updates. Taking a look at the update logs, I have updated all the applications including the app I used to check the integrity with the day before.
The hint for me was that the google play store it self did show it passed.
As it turned out individual apps where not passing the checks for some ungodly reason.
I hope this can help you too.
EDIT: I just reinstalled some of the apps that had issues passing the check from the Aurora store.
This caused the issues to return. Before the graphene update I did not have issues with the integrity check from apps installed through the Aurora store.