I've got the same problem but my problem is I'm on tour with Modul8 and I need my modules to be stored when i back up my projects. I can't waste my time to download and set each one every time I'll start my project.
I have the same problem even with the patched 2.9.2 Version on El Capitan. When it starts it doesn't show up any modules. It is also weird that when I click "About Modul8..." it does show that it's the educational version - even though I did update the registration information.
Ensure that you don't run Modul8 form the DMG archive . sometime when you firstlaucnh modul8 when downloaded you run it form the archive and after you create a short link to the dock. Modul8 cannot write modifications on the .dmg archive