I'm on a Bluehost shared server and Super Cache was working fine with all previous versions of WP back into the 2.5 series all the way through the 2.7 trunk builds until a few days ago when the cached pages stopped being served altogether. Nothing changed on my server with the exception of the MySQL database being upgraded from 5.0.45-community to 5.0.67-community and I really don't think that was the problem.
I've been running PHP 5.2.6 (fastcgi) with no problem either until the last few trunk builds (via the "Stay Updated" link) prior to RC1 when the plugin simply stopped working. At RC1, I enabled "compression" on Super Cache's settings page and the plugin started working again. This makes no sense to me.
Yesterday, I upgraded a client's site from 2.6.3 to 2.6.5 and Super Cache simply stopped working for her as well and enabling compression, uninstalling and reinstalling Super Cache, re-entering the .htaccess rules had no effect. I just left the plugin activated and logged out since her site was still loading fast enough (.55* average). She's running the same MySQL and PHP versions as I am on a different Bluehost server entirely.
Just on a whim I checked her site's source code this morning and there was the Super Cache entry at the bottom just like it should be and just like it wasn't the day before. Nothing changed at all overnight.
No errors in the error logs. No errors in the Apache logs. Nothing to give me a clue as to what went wrong. Paleo Pat and the others who had problems do not run on Bluehost that I know of and most likely have different set ups then myself and my client. Some folks are having problems and some are not (all running either 2.6.5 or 2.7 trunk or RC1)
Ghost in the machine?
And many thanks for this most excellent plugin. Us shared server bloggers would be lost without it.