As recommended in http://piwik.org/faq/how-to/#faq_59 , I deleted all piwik_archive_* tables with phpmyadmin in order to take into account the geoip data I have in consecuence of the installation of pecl geoip extension.
After some hours I could see that all the logs are regenerated (I have a cron job running every 15 minutes), except for the weekly ones: in the "Evolution over the period" graph I have data > 0 only for the last two weeks; all the preceeding weeks show 0 value.
Instead, the daily, monthly and weekly data are regenerated correctly
I tried again from the command line, deleting the db tables and running again the command
$ sudo -u www-data /usr/bin/php5 /var/www/piwik/misc/cron/archive.php --url=http://my.server.org/piwik/ --force-all-websites --force-all-periods=10000
it ran without errors on all my 14 websites (2 of them have about 2.000 and 20.000 daily visits), and I got everything but weekly reports fine: weekly data are reprocessed for no more than the last 52 weeks. Older weekly data are all zero.
Thanks for the report, Fixed in