I used xml sitemap generator a couple of months ago and it seemed to work great on a 5000+ page site.
I recently changed the linking structure on my pages to be root relative instead of document relative because of issues I saw in Google Webmaster Tools. It appeared that Google could not figure out how to go up 2 levels to find a directory. Forums I read suggested root relative URLS vs document relative URLS.
I use server-side inlcudes on my pages for topic navigation. The SSI's also use either root relative or full path absolute links. I made no changes to SSI files.
I just tried running xml sitemap generator and it went bonkers. It was spidering pages like:
I was able to clobber the program - it had gotten up to 21,000+ pages indexed. Am I breaking my site by changing the links? What do you think the problem is? Would adding a base href tag to each page help?