When using App-V Applications in Configmgr 2012 , make sure you have App-V client 4.6 SP1 CU5 deployed as this is the minimum supported version in CM12 .
Just a reminder when you are in a migration phase … First upgrade your App-V client software to version 4.6 SP1 CU5
This will also be a requirement is you want to add the App-V client as a dependency of your Application’s deployment type (app-V)
Hope it Helps ,
Kenny buntinx
