[Pisces]

To make the academy mission succeed and count you need to tell the game you want to do the exam. If not it thinks you want to just train it. It's on the screen before the mission is loaded. Choose exam instead of training. Then press start.

[Edit] Succeeding the academy missions as exams should give you a bit of starting renown during the campaign. (1500 iirc, but that may depend on what mods you have) Not that you can do much with it as you begin since any modification to the uboat or crew before the first patrol can get you to loose the renown you earn during the patrol. (stock bug) But before the 2nd patrol you can use it to recruite more experienced crew or other upgrades.