Multisite Piwik configuration?

I have a multisite wordpress installation with 50 to 100 sites. A installation of Piwik parallel to wordpress has been tracking all of them flawlessly over the last two years. My site’s url is http://blog-net.ch

But since several weeks, maybe even months (I am not checking every aspect of this installation too regularly, the whole thing is more of a hobby to me), some site owners start complaining that their statistics seem to be empty now. In the Piwik “All sites” list, now I find many sites multiple times, sometimes 20 times or more.

The wp-piwik ist installed and activated for all sites.

Am I doing it wrong? I think the problem started either since a certain plugin version or since a certain piwik version, but I can’t tell which.

Can anybody help me?

https://wordpress.org/plugins/wp-piwik/