Seems like you solved the problem yourself - well done. Just one minor thing: You definitely should download ez 3.8.6 as this is a bugfix for an ezxml problem in 3.8.5 so you might save yourself some trouble.
Didn't solve the problem, yet. Try the above link where it says "doesn't work" and try the same domain with the additional index.php. One works, the other doesn't.
I get the same page for
http://stories.bizmag.de/ and http://stories.bizmag.de/index.php
which is page with the heading wirtschaftswunder, a horizontal menu, an access denied message and a login window. The debug messages also look quite similar except for the line "Error ocurred using URI: /index.php" which is just "Error ocurred using URI: /" for the first url.
The most likely reason for unexplained stuff is the cache function of ez. Sometimes you change something in an ini file and forget to empty the cache or you empty the cache only partially and if you do sometimes later you see the result of all multiple changes at once.
The source of your problem was most likely in the siteaccess settings in the override site.ini.append.php or the site access specific site.ini.append.php although this is hard to say for sure afterwards.