[Plugin: Google XML Sitemaps] Sitemap.xml doesn’t contain custom permalinks

I am using a permalink structure in WordPress that creates urls such as:

http://blog.mike-hays.net/write-host-hello-world/

These are sometimes called “pretty permalinks”. I’m using a url rewriter similar to mod_rewrite to make this work.

But the Google Sitemap Generator generates a sitemap.xml with a link similar to the following:

http://blog.mike-hays.net/index.php/write-host-hello-world/

These are sometimes called “almost pretty permalinks”. The almost pretty permalinks are what are showing up in Google. The almost pretty permalink “works” but it isn’t my desired state.

Can you tell me how to configure Google Sitemap Generator to create a sitemap with my “pretty permalinks”?