I have multisite installed with buddypress.
On the main site all works 100% and I can view all the subdomain stats from admin panel.
The problem is when a subdomain user would like to view their stats, they can see the widgets but no stats.
I have created the sites in the piwik admin panel and in the users piwik setting I have added the id of the site for piwik counter, but no luck. And after I have added the extra sites in the piwik admin my site became very slow, locally.
http://wordpress.org/extend/plugins/wp-piwik/
Sounds like a role-depending problem. I never tried BuddyPress... maybe the BuddyPress' rights management differs from "simple" WordPress'?
If tracking and the admin's stats page work fine, I won't expect a problem between Piwik and WP-Piwik.
I don't understand your last two sentences. Did you change IDs in the WP-Piwik database configuration? Or did you add the tracking code manually? WordPress becomes slow if you add sites to Piwik manually?
Please differ between WP-Piwik and Piwik in your descriptions.
The last 2 sentences was actually referring to an additional plugin for piwik, to show stats in the front-end. Sorry my bad.
So if I understand you correctly, I should manually ad site to piwik, but rather that wp-piwik do it for me.
No, WP-Piwik should work if you ad your sites manually as well as you ask WP-Piwik to add them automatically.
Following your description WP-Piwik seems to work properly but users can't access their own stats. Did you try to enable all roles in the config's "Display to:" section?