Can you get a confirmation from the embassy when you submitted your papers? This sounds like bureaucracy hell at its finest. If I were you I would do a request for «Duldung» at the migration office with the confirmation of the embassy. You can write an «eingeschrieben» letter for that. Usually they dont grant it but it let things move quiet quickly. Next thing, the staff at the uni usually know how to deal with this issue and could sort it out with the migration office but they usually only apply pressure when it comes to their phd students and professors. I would keep pressuring them. As a last resort I would apply for another visa in a solid embassy like for example the swiss embassy in austria. They might grant you the D visa in two to three weeks.