I still don't quite understand it but it seems to be related to a problem that has been discussed on the mailing lists back in September (starts with "portal.php and Google"
here).
In the end, changing portal.php to send a 301 instead of a 302 fixed the problem (even for the links that Google had already indexed).
Geeklog 1.3.10 ships with a portal.php that sends a 301 redirect.
bye, Dirk