I'm using the latest WPSC 0.9.9.6 on a site which delivers the Home Page via WordPress, but there are hundreds of "legacy" files not yet incorporated into WP. I have WPSC set to php cache.
When I attempt to access http://www.peterwade.com/archive/pw46.shtml in my browser, for example, I get a "Not Found" page in WP, yet the file is on the site. WP is in the /assets/ folder. When I go to my Newsletter page and click on the link there for issue 46, the file displays.
Removing the WPSC entries from .htaccess seems to solve the problem but I'm not sure if the home page is cached now.