WP Super Cache caching very few pages on Multisite

What could be preventing my 1,500-site WordPress network from caching more than 15 pages? The plugin is reporting the following:

Cached pages since Mar 9, 2012 : 15
Newest Cached Pages:
1. /
2. /
3. /
4. /
5. /
6. /
7. /
8. /blog/2011/05/
9. /
10. /

The “Contents” tab in WP Super Cache settings shows this upon stats regeneration:

WP-Cache (0KB)

WP-Super-Cache (24.05KB)
2 Cached Pages

When I show the file list here, it provides these:

1. authorsxpress.com/.needs-rebuild 684
2. authorsxpress.com/index-mobile.html.needs-rebuild 684

This is the highest number of pages I’ve seen WP Super Cache actually cache on this network for the last several months. Yes, I know I’m an idiot for just now getting to this. By the way, APC (along with the associated WP plugin) *was* installed, but it started causing a variety of stability issues (though everything was noticeably quicker), so it was removed a few days ago at least temporarily.

WP Super Cache settings: Preload mode is ON, Cache hits... ON, Use mod_rewrite... ON, Compress pages... OFF (due to resource consumption), Don't cache pages for known users ON, Make known users anonymous... OFF, Cache rebuild... ON, Clear all caches files when a post or page is published or updated ON, Extra homepage checks... ON, Only refresh...when comments made OFF, List the newest cached... ON, Coarse file locking... OFF, Late init... OFF, Cache Timeout 3600: Scheduler Clock 00:00 hourly.

Accepted Filenames & Rejected URLs:
Do not cache… Search Pages, wp-.*\.php
Filesnames that can be cached even… wp-comments-popup.php, wp-links-opml.php, wp-locations.php, feed, atom, rss, rdf
Rejected User Agents… bot, ia_archive, slurp, crawl, spider, Yandex

I’m on a VPS: MediaTemple DV 4.0, Plesk 10, CentOS 5.

http://wordpress.org/extend/plugins/wp-super-cache/