As pointed in http://social.technet.microsoft.com/Forums/windowsserver/en-US/5e6dc56d-9069-42e3-a7e3-87437cf8ed81/scheduled-tasks-run-in-the-default-user-profile ( No answer from microsoft yet )
I'm having the same issue. A scheduled task that we used to run perfectly in windows server 2008R2, does not execute in windows server 2012. The executable of this task, depends on user environment folders.
Even if the task has an user account specified, when ran without being logged in to the server it executes against the default profile, so the user enviroment folders are not the correct ones and the executable fails.
Somebody knows how to fix this?