I'm on the latest version of WP and W3TC. \
I've tried disabling all other plugins.
Page cache rewriting seems to be working fine, as does the standard url rewriting for WP "pretty permalinks"
I've got rewrite logging on and error logging set to "debug" but the only errors I get when trying to load the minified css/js with minify URL Rewriting turned on is just that those files don't exist.
I even turned off all modules except for minify to make sure that there wasn't some kind of conflict with gzip somewhere.
The strange thing is that rewriting seems to be working some of the time, just not all the time (though the error never actually goes away)
When I say it's "working" i mean when I load the page and see the reference, remove the ?file= from the url and sometimes the file loads up, and sometimes I get a 404.
I've got a few other sites on shared hosting where this plugin works flawlessly, so I know it's something with my server config, I'm just not sure what.
The proper .htaccess file is in the minify directory and I even went as far as setting the permissions on it to 777.