Hi Al,
there is no problem with crawling a site with mod_rewrite rules with sitemap generator. It acts exactly as SE bot does and just retrieves the URLs found on your pages.
I believe the problem is that you have the following tag:
<base href='[ External links are visible to logged in users only ]
Generator supports the <base> tag, but the attributes should be enclosed in double quotes ("). For the moment you can replace this line with:
<base href="[ External links are visible to logged in users only ]">
The next version of generator will work with both quotes types.