Ok, I found the culprit. The difference is in the OPF, specifically the metadata tag. In the my test-book I have:
Code:
<opf:metadata xmlns:opf="http://www.idpf.org/2007/opf" xmlns:dc="http://purl.org/dc/elements/1.1/">
...
</opf:metadata>
If I remove the red part, it does work. The tag is valid though as far as I know.
So, it appears that the OPF is not copied, but recreated.