SEO optimized urls don't show in Piwik

Pages on our website are using a URLRewrite module serverside. So clientside for javascript, the url should be read like the SEO url is shown in the address bar.
But why is every page in piwik shown as the original url which now should be used on the background only??
I am missing something I guess…

Piwik is not able to access the non friendly URL so you might be looking at old data, before you switched to friendly URLs. Make sure you select today in the calendar.

Strange as my page friendly urls are working for months now…
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