I did run the upgrade script yes, what I figured out so far is that now I switched back to the English language, I can, to some extend, use the blocks again.
( Well, the ones that have not disapeared, which is a surprise for me too. )
I normally use the Netherish language (Also known as Dutch)
And it was set to that during the Update proces. Seems that it was there were it wend wrong.
Now my guess about the current lost blocks is this.
As it is a form where to choose from, in the blocks part at the admin backend, when there is no translation in the current used language, there is no proper form-result send.
So the system falls back on the main module: system, and it's blocks.
My next trial and error will be translating and the switching to my native language again. In theory this should fix it...
Except for the lost Blocks