Finally I tracked down the problem of the wrong admin urls.
The Core/Frameworks/Flake/Framework.php wrongfully detect the base url of the site. Although the problem is not with the Framework.php but with the php version included with dsm 5.0. There is a problem with a php function named substr_compare which is compares to strings but it always return true even if the searched string not included in the base string. This specific function used for testing the url if it's includes the actual php script's name (mostly index.php) or not to decide to cut it off or not from the request uri. So if you try to access the admin like this
http://[hostname]/baikal/admin/index.php it will work until the url has the index.php ending. But if you not specify the index.php at the end it won't.
So to fix this (more precisely to make a workaround) you have to edit the referred php script and replace the endsWith function (line 81) to this one:
PHP:
public static function endsWith($sString, $sTest) {
$iTestLen = strlen($sTest);
if ($iTestLen > strlen($sString)) return false;
//this is the original line: return substr_compare($sString, $sTest, -$iTestLen) === 0;
return substr($sString, -$iTestLen) == $sTest;
}
After this the admin site will function normally without further modification of admin/index.php