I am having a similar problem: 2 multisites on the same server with the exact same httpd settings. The only difference is that one runs a bunch of multisites and has over 40 plugins activated, the other one is a fresh install with only 4 plugins activated.
The one with less plugins works. Can you guys check if you have any of my plugins installed, so we can narrow it down? Unfortunately, I can't deactivate and reactivate all the plugins, as I run a busy multisite and can't play around with it...
Add Cloned Sites for WPMU (batch)
With this plugin you can simply batch add a bunch of domain names / sites to your WPMU install and use one of your existing sites as a template for the new sites. The existing blog will be cloned exactly including posts, layout, settings, etc. The plugin also takes care of domainmapping the newly created sites. (needs 'WordPress MU Domain Mapping' by Donncha to be installed). New is the option to clone without domainmapping, so pure cloning in batch! Please donate after each batch, I do need the caffeine, thanks!
Version 0.8.4.2 | By Frits Jan van Kempen | Visit plugin site
AVH Extended Categories WidgetsAVH Extended Categories Widgets
Replacement of the category widget to allow for greater customization of the category widget.
Version 3.6.5 | By Peter van der Does | Visit plugin site
WordPress Backup and more...
Version 2.1.15 | By Daniel Hüsken | Visit plugin site | FAQ | Support | Donate
Better WordPress MinifyBetter WordPress Minify
Allows you to minify your CSS and JS files for faster page loading for visitors. This plugin uses the PHP library Minify and relies on WordPress's enqueueing system rather than the output buffer (will not break your website in most cases). This plugin is very customizable and easy to use.
Version 1.2.0 | By Khang Minh | Visit plugin site
Better WP SecurityBetter WP Security
Helps protect your WordPress installation from attackers. Hardens standard WordPress security by hiding vital areas of your site, protecting access to important files via htaccess, preventing brute-force login attempts, detecting attack attempts, and more.
Version 3.4.4 | By Bit51.com | Visit plugin site
Broken Link CheckerBroken Link Checker
Checks your blog for broken links and missing images and notifies you on the dashboard if any are found.
Version 1.6.2 | By Janis Elsts | Visit plugin site
BWP Google XML SitemapsBWP Google XML Sitemaps
A more lightweight Google XML Sitemap WordPress plugin that generates a Sitemap index rather than a single sitemap. Despite its simplicity, it is still very powerful and has plenty of options to choose.
Version 1.2.1 | By Khang Minh | Visit plugin site
Content Aware SidebarsContent Aware Sidebars
Manage and show sidebars according to the content being viewed.
Version 1.1 | By Joachim Jensen | Visit plugin site
Convert Post TypesConvert Post Types
A bulk conversion utility for post types.
Version 1.2 | By Stephanie Leary | Visit plugin site
CSV to SortTableCSV to SortTable
Import data from a CSV file and display it in a sortable table using a simple shortcode.
Version 3.1 | By Shaun Scovil | Visit plugin site
Custom Widget AreaCustom Widget Area
A simple plugin to create custom widget area.
Version 1.1 | By Shakti Kumar | Visit plugin site
Dave's WordPress Live SearchDave's WordPress Live Search
Adds "live search" functionality to your WordPress site. Uses the built-in search and jQuery.
Version 2.8 | By Dave Ross | Visit plugin site
Duplicate PostDuplicate Post
Clone posts and pages.
Version 2.4.1 | By Enrico Battocchi | Visit plugin site | Donate | Translate
Executes <?php ?> code in your posts, pages and text widgets.
Version 4.9 | By Sören Weber | Visit plugin site
Fast Secure Contact FormFast Secure Contact Form
Fast Secure Contact Form for WordPress. The contact form lets your visitors send you a quick E-mail message. Super customizable with a multi-form feature, optional extra fields, and an option to redirect visitors to any URL after the message is sent. Includes CAPTCHA and Akismet support to block all common spammer tactics. Spam is no longer a problem. Settings | Donate
Version 184.108.40.206 | By Mike Challis | Visit plugin site
Flexi Pages WidgetFlexi Pages Widget
A highly configurable WordPress sidebar widget to list pages and sub-pages. User friendly widget control comes with various options.
Version 1.6.10 | By Srini G | Visit plugin site
HTML Import 2HTML Import 2
Imports well-formed static HTML files into WordPress posts or pages. Supports Dreamweaver templates and Word HTML cleanup. Visit the settings page to get started. See the User Guide for details.
Version 2.2 | By Stephanie Leary | Visit plugin site
Version 3.6 | By Aakash Chakravarthy | Visit plugin site
jQuery ColorboxjQuery Colorbox
Used to overlay images on the current page. Images in one post are grouped automatically.
Version 4.4.1 | By Arne Franken | Visit plugin site
Link LibraryLink Library
Display links on pages with a variety of options
Version 5.5 | By Yannick Lefebvre | Visit plugin site
ManageWP - WorkerManageWP - Worker
Network Activate | Edit
Manage all your blogs from one dashboard. Visit ManageWP.com to sign up.
Version 3.9.22 | By ManageWP | Visit plugin site
Multisite Plugin ManagerMultisite Plugin Manager
The essential plugin for every multisite install! Manage plugin access permissions across your entire multisite network.
Version 3.1.2 | By Aaron Edwards | Visit plugin site
Multisite Robots.txt Manager | MS Robots.txtMultisite Robots.txt Manager | MS Robots.txt
A Multisite Network Robots.txt Manager. Quickly manage your Network Websites robots.txt files from a single administration area.
Version 0.2.0 | By tribalNerd | Visit plugin site | Settings | F.A.Q. | Support | Feedback | Donations
Network Plugin AuditorNetwork Plugin Auditor
Add a column to your network admin to show which sites have each plugin active (on the plugin page), and which plugins are active on each site (on the sites page), and the active theme on each blog (on the themes page).
Version 1.2 | By Katherine Semel | Visit plugin site
Posts By TagPosts By Tag
Provide sidebar widgets that can be used to display posts from a set of tags in the sidebar.
Version 2.7.1 | By Sudar | Visit plugin site
Proper Network ActivationProper Network Activation
Use the network activation feature of WP MultiSite without problems
Version 1.0.4 | By scribu | Visit plugin site
Quick CacheQuick Cache
Dramatically improves the performance & speed of your site! Also compatible with WordPress® Multisite/Networking.
Version 111203 | By PriMoThemes.com / WebSharks, Inc. | Visit plugin site
Manage all your 301 redirects and monitor 404 errors
Version 2.2.13 | By John Godley | Visit plugin site
Regenerate ThumbnailsRegenerate Thumbnails
Allows you to regenerate all thumbnails after changing the thumbnail sizes.
Version 2.2.3 | By Viper007Bond | Visit plugin site
This plugin replaces WordPress search with a relevance-sorting search.
Version 3.0.5 | By Mikko Saari | Visit plugin site
Revision ControlRevision Control
Allows finer control over the number of Revisions stored on a global & per-type/page basis.
Version 2.1 | By Dion Hulse | Visit plugin site
SEO Friendly ImagesSEO Friendly Images
Automatically adds alt and title attributes to all your images. Improves traffic from search results and makes them W3C/xHTML valid as well.
Version 2.7.3 | By Vladimir Prelovac | Visit plugin site
SEO Smart LinksSEO Smart Links
SEO Smart Links provides automatic SEO benefits for your site in addition to custom keyword lists, nofollow and much more.
Version 2.7.5 | By Vladimir Prelovac | Visit plugin site
SEO UltimateSEO Ultimate
This all-in-one SEO plugin gives you control over title tags, noindex/nofollow, meta tags, rich snippets, slugs, canonical tags, autolinks, 404 errors, rich snippets, and more.
Version 7.5.7 | By SEO Design Solutions | Visit plugin site
Simple TagsSimple Tags
Extended Tagging for WordPress 3.1 : Suggested Tags, Mass edit tags, Auto-tags, Autocompletion, Related Posts etc. NOW Compatible custom post type and custom taxonomy !
Version 2.2 | By Amaury BALMER | Visit plugin site
Site Replicator for WordPress networksSite Replicator for WordPress networks
Allows super admin to create a new sub site which is a copy of an existing sub site.
Version 0.5 | By Ron Rennick | Visit plugin site
Automatically add links on your posts, pages and RSS feed to your favorite social bookmarking sites.
Version 220.127.116.11 | By Blogplay | Visit plugin site
Sort My-SitesSort My-Sites
Sorts the My Sites listing on both the page and in the 3.3 admin bar dropdown
Ultimate tag cloud widgetUltimate tag cloud widget
This plugin aims to be the most configurable tag cloud widget out there, able to suit all your wierd tag cloud needs.
Version 1.3.17 | By Rickard Andersson | Visit plugin site
WCK Post Type CreatorWCK Post Type Creator
Creates Custom Post Types for WordPress
Version 1.0 | By Reflection Media, Madalin Ungureanu
Web Ninja Auto Tagging SystemWeb Ninja Auto Tagging System
This plugin will automatically make tags with the tagthe.net and yahoo yql services when you save or update a post. Also has the option for retagging all post.
Version 1.0.4 | By Josh Fowler | Visit plugin site
Web Ninja Google AnalyticsWeb Ninja Google Analytics
Enable Google Analytics on all of your pages instantly and add Google Analytics Stats to your Admin Dashboard and Posts. Can track external links, mailto links, and download links on your site.
Version 1.0.9 | By Josh Fowler | Visit plugin site
WordPress MU Domain MappingWordPress MU Domain Mapping
Map any blog on a WordPress website to another domain.
Version 0.5.4.2 | By Donncha O Caoimh | Visit plugin site
Display your host's PHP, MYSQL & memcached (if installed) information on your WordPress dashboard.
Version 1.60 | By Lester 'GaMerZ' Chan | Visit plugin site
WP Category Post List WidgetWP Category Post List Widget
Lists down Posts filtered by category. You can show thumbnail, modify the HTML structure of the widget and do almost whatever you want. Access it from the Widgets option under the Appearance. The shortcode is [wp_cpl_sc] Check the settings page for more info or check the documentation here
Version 2.0.3 | By Swashata | Visit plugin site
WP Overview (lite) MSWP Overview (lite) MS
Show Dashboard Overview and footer memory usage with less consumption on Network Multi~Site Environment. Work under GPLv2 License. | Donate | WP Overview? | WP Missed Schedule? | Admin Bar Removal? | Admin Bar Node Removal? | ToolBar Removal? | ToolBar Node Removal? | LogIn DeIndexing? | WP DeIndexing? | Enhancer IE Surfing?
Version 2010.0925.0254-MS | By sLa | Visit plugin site
WP SortTableWP SortTable
Create a sortable table using a simple shortcode. The table may contain a filtered index of Posts, Pages, or Custom Post Types -OR- data from a CSV file -OR- data from a Google Spreadsheet.
Version 0.9.4 | By Shaun Scovil | Visit plugin site