You can use Profile management 5.x in the same environment as Microsoft Application Virtualization 5.0 (App-V 5.0).
You must exclude the following item using Profile management exclusions:
If you don't exclude these items, App-V applications work the first time users access them but they fail, with an error, on subsequent logons. For instructions on setting exclusions, see To include and exclude items.
If the UserLogonRefresh setting is enabled in App-V, disable the Profile streaming policy in Profile management.
For an example of how to sequence an App-V application, see http://support.microsoft.com/kb/2830069.
For information on configuring third-party Profile management solutions with App-V enabled, see https://technet.microsoft.com/en-us/library/dn659478.aspx. Do not include Software\Classes on Microsoft Windows 10 systems.