I had the same problem a few months ago, but that wasn't happen in all cases. For some cases the task to run again the initial whitelisting resolidify all the system. Run commends -> sadmin so and then the system will resolidify all the system, but for some other cases we need to reinstall the application from the scrach.
Hope it helps
What version of Application control you are running?
If you are running Application control 6.1.2 or later try to unsolidify the complete volume (Exampe - C:\) and solidify again and check if your issue is fixed.
You can run the above as a client task so that you don't need to go and do it on individual systems.