Tracking links and [usertrack] not working

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
It appends only to the root domain - - so the clicked link leads to instead.
Also the [usertrack] doesn’t track anything.

Hope someone here will help me with these issues.

Thank you.