In the install.php and in a number of the other scripts the server variable 'DOCUMENT_ROOT'
$htaccess_path = $_SERVER['DOCUMENT_ROOT'].$htaccess;
Apache supports a reasonably new commonly used system called "VirtualDocumentRoot" where you can adjust the document root based on the domain name etc... A problem with this is that apache always returns just /htdocs when you access the DOCUMENT_ROOT variable. This causes your software to stop working entirely and wont even install because it can never find the correct path for the htaccess stuff. In my apache config file I have a line like this that sets the actual document root...
VirtualDocumentRoot /var/www-auto/%4.0.%5.0/%3.0/%2.0/%1.0
I have a solution! I put the following line in the top of your install.php and in your global.php I also put it into the db_config.php but I am not sure it needs to be there. I do not know how this would affect people not using a virtual domain system. You might need to put a switch into the install to toggle this on or off...
$_SERVER['DOCUMENT_ROOT'] = Str_Replace($_SERVER['SCRIPT_NAME'],"",$_SERVER['SCRIPT_FILENAME']);