Problem is, I upgraded via the Backend to 0.8.5 and changed wp-piwik_wpmu immediately to true. After that the plugin created new entries in Piwik for all sites in the network again instead of picking up the existing entries created with 0.8.4. Users now aren't able to see their statistics before the upgrade in the Backend and WP-Piwik puts in the tracking code for the newly created sites.
So are there any infos on the correct update procedure for a multisite installation so it picks up the already created sites instead of creating double entries?
Nevertheless a great plugin, thanks for the effort!