I have to admit I'm a little baffled. I have Piwik and WP-Piwik running on three WordPress installations. One Installation shows some strange behaviour. I don't know what matters, so I'll just write down everything I can think of.
It's a multisite installation with different four sites on three different domains. On the main blog http://www.aaa.de WP-Piwik works fine. Today we noticed that on http://www.bbb.de and on http://www.ccc.de the statistics don't work and the settings page shows the error
An error occured: Please check URL and auth token. You need at least view access to one site.
Funny thing is, the plugin is actually working, the visitors of both sites are tracked by Piwik (and there is no manual tracking code), it's just the admin area that's messed up.
The token and the URL are identical to the http://www.aaa.de installation, where it works fine. The token is from the admin account (not recommended, I know, it was set up in a hurry).
While trying to debug it we actived the plugin for a fourth site, which wasn't tracked yet. We entered the same URL and token, checked "auto-configuration" and hit save. The site was created in Piwik, and the plugin works there as well. On a side note, while both non-working sites are on different domains, this particular site is a subdirectory of the main blog (www.aaa.de/ddd/).
I tried disabling and enabling the plugin, uninstalled and reinstalled it, hoping that it would clean it's database entried, but to no avail.
I even added a new user on Piwik and used his token, but here again no change.
Used versions: WordPress 3.3.1, Piwik 1.7.1, WP-Piwik 0.9.1