After a lot of try and error I found that obviously iUpgradeable has not been fired correctly in one of my updates before. I fisrt figured that I didn't have the correct permission keys in the permissions table (easy to fix) and then found that the upgrade procedure in iUpgradeable had tried multiple times to transform old permissions into the new ones. I actually had ~12.000 permission entries in my forum_permission table :-)
My trick was to force iUpgradeble to run once again. I first deleted all entries in the forum_permission table and made sure that the two importan permssion key entries (found at the the beginning of this thread) are in place.
I then changed the UpgradeModule() method to fire for the version I was about to install and it indeed fired correctly and moved all forum permissions correctly.
I think I read a long time ago that trusting iUpgradeable to fire correctly is not so good, it simply does not seem to run in every case.
Anyway, I'm up and running again.