PHP just logged the following error at an offline test site where WP Super Cache has been running without problems. I am posting this information in case it sheds light on the cause of problems others have been having.
The Logged Error
[01-Jun-2012 14:31:10] PHP Fatal error: Call to undefined function wp_cache_phase2_clean_expired() in C:\public\www.subsn.com\wp-content\plugins\wp-super-cache\wp-cache.php on line 2893
APC Opcode Caching enabled
APC User Caching enabled via object-cache.php
Autoptimize (my own custom version with various fixes)
Super Cache current trunk version
mod_rewrite Mode enabled
All SC recommended options selected, except preload was off
2583 pages cached (6 WordPress, the rest a custom post type)
The error occurred when I tried to load a new page that wasn't cached. Firefox locked up. Firefox wasn't functional even after closing and reopening it until I cleared its cache. Returning to the page locked-up Firefox again and its cache had to be cleared again.
Clearing the APC User cache didn't clear the problem. Clearing the APC Opcode cache didn't clear the problem.
Windows Task Manager indications on the server suggested that Apache was executing an endless loop. Restarting Apache cleared the problem. However, Apache took about two minutes to stop, before it could be restarted, which is another indication that it was locked in a loop.
After restarting Apache I went back to the same uncached webpage with Firefox. Super Cache cached the page and it now displays normally.
My configuration is of course significantly different than others have and there are many potential issues outside of Super Cache. Even so, Super Cache has been running very reliably with this configuration during extensive stress-testing, so the error seems significant.