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Tracking links and [usertrack] not working

Hi,
I just upgraded to 3.5.5 version.
When someone click on a content link it redirects to my 404 page.
It seems that the tracking code doesn’t append to the complete url of the installation which is http://my.site/list/.
It appends only to the root domain - my.site - so the clicked link leads to my.site/404.html instead.
Also the [usertrack] doesn’t track anything.

Hope someone here will help me with these issues.

Thank you.
Adi