The index.php can NOT be 0 byte.
Perhaps you have to check the permission to understand why it is a zero byte.
Is this a link ?

If you want that we have a look on your server and try debug why Joomla declare this JCacheController twice and return you a 0 byte, this is also possible with our billable support that you can order at www.jms2win.com/download?page=shop.produ...35&category_id=1

As Joomla has release a beta 6, perhaps you could also try with this very.

The administrator/index.php file was not 0 bytes. But, MultiSites was trying to download index.php as a 0 byte file.

I finally fixed this problem by restarting apache.

Now I can get to the Manage Sites page and install the patches.

With the patches installed everything looks like it works except for the Layouts. It causes this error:

Warning: InstallerController::require_once(/var/lampp/1.6.4/htdocs/Joomla-1.6-Beta5/administrator/components/com_multisites/helpers/installer.php) [function.InstallerController-require-once]: failed to open stream: No such file or directory in /var/lampp/1.6.4/htdocs/Joomla-1.6-Beta5/administrator/components/com_installer/controller.php on line 35

Fatal error: InstallerController::require_once() [function.require]: Failed opening required '/var/lampp/1.6.4/htdocs/Joomla-1.6-Beta5/administrator/components/com_multisites/helpers/installer.php' (include_path='.:/opt/lampp/lib/php') in /var/lampp/1.6.4/htdocs/Joomla-1.6-Beta5/administrator/components/com_installer/controller.php on line 35


# ls -l /var/lampp/1.6.4/htdocs/Joomla-1.6-Beta5/administrator/components/com_multisites/helpers/
total 52
-rw-r--r-- 1 nobody nobody 37422 2010-08-03 11:59 helper.php
-rw-r--r-- 1 nobody nobody 44 2010-08-03 11:59 index.html

no installer.php in that directory.

Edwin,
Is the 1.2.34 ok to use with this problem with the Layouts?

It looks like it is missing the 'installer.php' file in the helpers directory.

YES the layout menu is still not work and will not work yet in JMS 1.2.35 that we will release soon.
We have not yet found how to have something compatible between Joomla 1.5 and 1.6 for this part.
You can use the layout in the front-end but you can not install additional layout in 1.6.
As we have not yet published additional layout, we given a lower priority to this part.

I remember you that we still consider JMS 1.2.34 as an alpha for Joomla 1.6.
See the release note that mention what is supposed working correctly.
www.jms2win.com/faq/change-history-v12x
A full Joomla 1.5 and 1.6 is not yet available and we working on it as you can see.