I just grabbed a book from the PG front page. The OPF has:
Code:
<dc:identifier opf:scheme="URI" id="id">http://www.gutenberg.org/63130</dc:identifier>
Which calibre will use to create the identifier:
Code:
uri:http://www.gutenberg.org/63130
Which expected and is correct.
From memory, older versions of calibre replaced the colon in URI and URL identifiers with the vertical bar. The current version will handle this, but, doesn't change it to a colon.
So, as I understand it, there is nothing wrong. It is working as designed.