Firstly, thanks so much for this software. Without it even our dedicated server was having problems running WordPress as a CMS.
One our our sites (We're on a WHM/Cpanel dedicated server) has multiple parked domains, though it all serves out the same information.
WP-Super-Cache creates a folder for each domain, and I guess this is fine as it's not really a lot of extra work or space but recently the "alternate" domains have stopped updating and continue to serve out old versions of the site until I do a manual "Delete Cache".
I have WP-Super-Cache set to clear the cache whenever a post or page is published, and for the main domain this works.
Domains in question:
http://www.l5r.com/ (Main domain, set in WordPress, works great with the cache)
http://www.legendofthefiverings.com/ (alternate domain, same directory, feeds the same files, ends up serving old cache until I manually click "Delete Cache".
I have fixed the "meta" typo that I found posted here, no idea if that has fixed the problem or even should, but other than that it's the vanilla latest version of WP-Super-cache.