The thing is the files shouldn’t be encrypted anymore. I deleted the whole user account and it’s files. Disabled the global encryption and created a new user, and did the upload afterwards. Currently it looks like that somehow remains of the encryption setup did persist. The question is where?
Could you look in your data directory and delete the encryption keys?
If you upload the same files (that were previously encrypted) in to the other user account ownCloud might get confused.
If this does not help please write down step by step what you did to get to your state.