This article provides information regarding Metaprofiles (MP) and Windows profiles relationship.
Quest Metaprofiles does not replace Windows profiles, nor it has anything to do with Windows profile creation process.
Quest MP is built around simple network client-server scheme, where MP agent (pnmpts) is acting as a client and MP file server (pnmpfs) is a server part.
After user logs into TS/RDSH/VDI machine, his profile is created/updated by Windows and only after that MP agent applies files and registry settings that specified in vWorkspace Management console for particular user/group/OU.
When user logs off, the opposite process happens, where MP agent extracts files and registry keys, then sends them to MP file server. After that MP agent will try to delete user's profile on TS/RDSH/VDI.
Important: this behavior is by design. Next time user will log in, profile will be created from scratch which may create an additional load on disk subsystem and user may lose some settings that weren't specified through User Profiles in vWorkspace Management console. That's why MP is usually used in environments, where users configured with mandatory profiles.