I have been fooling around a little more and figured out, that the above is not the only place where this problem occurs: This is also happening when I try to save changes in the setting menu:
Hitting “Save Changes” at
https://ssl.webpack.de/mydomain.de/wordpress/wp-admin/options-general.php
results in a new url
https://ssl.webpack.de/wordpress/wp-admin/options-general.php?settings-updated=true
which is again missing the “/mydomain.de” part.
This problem seems to occur at other places as well.
To me, it looks like this may be a dublicate of the following post:
link. However, that post is already one year old and it was said that the hotfix (which was unfortunately not detailed on) would be included in the next release.