It has nothing to do with Windows or it's viruses.
Already told you, that the phone went just fine until I had to restore my old backups. Also, other mass-storages work just fine, and the whole os works just fine.

Re-creating the folders using the phone doesn't work also (terminal mkdir, filecase).The folders get created, but the phone can't save stuff in them. Actually, if I set the config to save stuff in MyDocs, it works, but if I set it to use MyDocs/Pictures, it does not.

Windows can't change permissions because the phone set them on something else, and Windows can't access it the right way.

It is not a virus. The backup just messed up something pretty bad, yet noone can tell me what.