Are you opening this site from a bookmark? If so try to use the menu to navigate to the report as the URL changed. If not, try to update all the files manually (except config/config.ini.php) see http://piwik.org/docs/update/#the-manual-three-step-update

@tsteur no, I'm always using the menu. And according to the system integrity check, everything is ok. And I always update manually following the three step update.
Nevertheless I replaced the CustomVariables directory with the one from the 2.6.1 package and received a different error:

Fatal error: Class 'Piwik\Plugins\CustomVariables\Menu' not found

and this file indeed is missing (also currently here in the repo).

Menu.php from the backed up CustomVariables directory has the following function:

public function configureReportingMenu(MenuReporting $menu)
    {
        $menu->add('General_Visitors', 'CustomVariables_CustomVariables', array('module' => 'CustomVariables', 'action' => 'index'), $display = true, $order = 50);
    }

Seems that I'm missing a current menu file as it isn't provided by the package.
[edit] See e9aae52

It was in this case actually good to replace the whole CustomVariables directory but the caches were probably not cleared. It might be worth executing rm -rf tmp/cache/* after copying the folder. The Menu.php should not exist there.

To make this easier in the future I added a command ./console core:clear-caches.

@mattab Maybe we need a guide for this use case when a user copies the same files again of the same version again. As there is no component update (same version was already installed) the caches won't be cleared. I think the same happens when downgrading Piwik.

@tsteur thx a lot, works like a charm! ;-)