Endpoint Policy Manager should be reapplying my settings on application launch time. Why doesn't "reapply on launch" work ?
Reapply on launch requires KB3033929 (https://www.microsoft.com/en-us/download/details.aspx?id=46148)or Reapply on Launch (up to build 901.) 64-bit patch. 32-bit patch is found here: https://www.microsoft.com/en-pk/download/details.aspx?id=46078
After Netwrix Endpoint Policy Manager (formerly PolicyPak) CSE build 901, this patch is no longer required.