[Plugin: WP Super Cache] Mod_rewrite URL issue

I have been having some issues with mod_rewrite. I am running the latest WordPress and WP Super Cache. My site is hosted off of 2 servers connected over a crossover cable, one server is dedicated to SQL and the other to the rest of the installation.

When I activate mod_rewrite caching, the homepage url eventually changes to something like:
http://www.mysiteurl.com/wp-content/cache/supercache/www.mysiteurl.com/index.html

The subpages are all fine.

Thanks in advance

http://wordpress.org/extend/plugins/wp-super-cache/