Yes, this is a known problem many users complain about - there are at least 2 other threads and 2 bug reports already within the relatively short time from the release of the Kindle 3.1 software:
https://www.mobileread.com/forums/sho...d.php?t=120613
https://www.mobileread.com/forums/sho...d.php?t=122361
http://bugs.calibre-ebook.com/ticket/9147
http://bugs.calibre-ebook.com/ticket/9201
From the Calibre sources, it is not clear to me what could be the problem, it may require some additional reverse-engineering - which is may be the main reason why it is not sorted out.
It is perhaps promising that there exist third party produced mobi periodicals not suffering by the problem: Instapaper generated Kindle periodicals (except when Instapaper is used via Calibre - then the problem appears). Which means that either Marco reverse-engineered the format himself too or he uses some mobi generation tools that do not suffer by the problem.
At the moment, the only way to avoid the problem is disabling upgrade to Kindle 3.1 software - unless you already have it, of course.