Same issue. On my WMPU install, the cached files just don't get served. Inside of wp-content/cache/ there are files being created such as
I'm not sure, but isn't it supposed to go into the supercache directory? It's weird, because it creates empty folders inside the supercache folder that mimick the site structure, but the .html files are stored in the root of wp-content/cache with just different md5 hashes in the filename.
The .htaccess auto-updating thing seems a little buggy too, i had to do it manually because it was cutting off half of the code or wiping the .htaccess completely.
I've double checked permissions/ownership on all directories and files and made sure i was logged out and cleared my cookies when testing a cached page. I've tried with supercache on and off also, still doesn't served cached pages. I've made sure wp-config has the right define value and i even hardcoded the document root into the .htaccess file. All i can figure is either the .htaccess is not pointing to the cached files correctly or the cached files arent being stored in the right spot.