When upgrading our Targets (pvs & physical) I have noticed some strange behaviour, parts of configs didn't seem to bite, we have found that there is slight imprint that seems to be left by our old Agents? 8.3, which seems to stop occasional (not all) of the new config biting for users/machines etc. a complete uninstall and clean (registry/file system) then a fresh deployment seems to resolve this issue for us. im not saying there isn't something specifically environmental that is affecting these machines, but if it helps one person its worth mentioning :)
I've found sometimes with the 8.3 agents, that for some bizarre reason the permissions are removed from "C:\ProgramData\AppSense\Environment Manager" and thus fails to install a new config. I'm unable to take ownership, or give system ownership. Removing the agent is the only way I've found to fix the permissions.