I had an epifani. I went into the data folder and removed a mod (vampire lord larger wings) that was automatically added (steam workshop) when I first startet skyrim through its launcher.
The BSA of that mod gave some errors that MO complained about but then went away, I just remembered.
Removing only the BSA of said mod have MO functioning perfectly again. It reads the VFS just fine now. Re-adding the BSA reproduces the problem so I am certain it is to blame. I am however unable to reproduce the error message I got earlier.
Nevertheless thank you very much for you efforts to help me!!
