I had the same problem with a WPMU upgrade and was eventually able to hack together a solution. It turned out that nextgen's admin/wp25/upload.php script was dying. Here's what I did.
1. in the nextgen plugin code, move the function
function wpmu_enable_function($value)
from admin/wp25/admin.php to the bottom of admin/wp25/functions.php
2. add the line
include_once (NGGALLERY_ABSPATH. 'admin/wp25/functions.php');
at the top of admin/wp25/admin.php.
This will make that function available to admin/wp25/upload.php
3. In the wordpress code, edit wp-admin/admin.php and change
require_once('../wp-includes/class-snoopy.php');
to
require_once(ABSPATH . 'wp-includes/class-snoopy.php');
This will stop wordpress from throwing a different error that results from not being able to load class-snoopy when wp-admin/admin.php is included by nextgen gallery's upload.php. In general, changing wordpress core code is a bad idea. It might be better to modify the include_path within the plugin. But this is a hack solution that got batch uploading working for me.