If you downgrade to 0.9.9.18, you will automatically regain your settings. This doesn’t fix the problem, but you can at least reproduce your settings.
I’m getting the following exception as soon as I activate Tracking using 0.10.0.3 in a Network (both in the backend – in the WP-Piwik settings upon apply – and in the frontend – in the footer where the tracking code would usually appear):
Warning: html_entity_decode() expects parameter 1 to be string, array given in [...]/wp-content/plugins/wp-piwik/classes/WP_Piwik.php on line 1065
PS: I also lost all settings and the WP-Piwik network overview reports all pages as not yet created. So it seems like WP-Piwik is unable to determine the page ids.