Reported in the forums: http://forum.piwik.org/read.php?2,99402,page=1#msg-100639
Finally, someone found the problem:
Drupals Piwik module was/is pushing the SiteId as string: _paq.push(["setSiteId", "2"])
However, Piwik checks it using !== against a number, which always fails because it's compared against a string.
In 090fe54: fixes #3746 - Bug in overlay when using setSiteId with a string value