Hi,
I have the following installation:
nginx, fastCGI, php-fpm.
php-fpm lives in a chroot.

problem:
the update files are extracted to the wrong position if the php-fpm chroot is exactly the joomla-home:

/var/www/php_chroot/
                .../configuration.php
                .../administrator
                ...

After some debugging I found that the problem is the following:
JPATH_ROOT is "" and
JPATH_SITE is ""
but these are used in the reconstruction.php as the yip-extraction destination path. And if they are an empty string then the zip contents are extracted somewhere where the currently executing php-script lives:

/var/www/php_chroot/administrator/components/com_joomlaupdate

instead of directly in root ("/")

So I think, the bugfix would be to check whether JPATH_SITE is an emptu Strindg, and i this case to set it to "/" (root).

BTW everything works fine if the php-chroot is not the same as the joomla-home, say the joomla-home is one or more levels deeper like:

/var/www/php_chroot/docroot_joomla
                              .../configuration.php
                              .../administrator
                              ...

In this case
JPATH_ROOT is "/docroot_joomla" and
JPATH_SITE is "/docroot_joomla"

thanks,
ALex.