Theme header image multisite-unaware public uri

I just noticed that I have a problem with newly uploaded theme header images after a recent core update. The uploaded file is correctly placed in the blogs.dir, the image paths in the backend also work nicely BUT the public path is missing the “files/” prefix.

e.G.:
http://nierenentzündung.com/2012/11/Nierenentzuendung.png is the public uri and, of course, not working.

http://nierenentzündung.com/files/2012/11/Nierenentzuendung.png works as intended.

Article images are not affected, only the standard header image upload for themes.

I have tried different themes, with no avail, therefore the culprit has to be something else, any ideas what could be the cause?