After updating Piwik I realized that it is not showing any data, except the header and footer. The problem was my really low end box (Sheevaplug). It was so slow, that execution was stopped. Looking in /var/log/apache2/error.log I found those lines:
[Tue Dec 24 17:14:25 2013] [error] [client 126.96.36.199] PHP Fatal error: Maximum execution time of 30 seconds exceeded in /path/to/piwik/vendor/tedivm/jshrink/src/JShrink/Minifier.php on line 467, referer: http://no.referer.org
The “max_execution_time” can be set in two .ini files, depending on the PHP parent process. If ran from Apache, then /etc/php5/apache2/php.ini is used, if started from command line /etc/php5/cli/php.ini is used. I double execution time in both and Piwik works (slow and) fine again.