John,
We haven't heard of it spamming like that before, but Facebook does try to re-crawl every page of your site that uses Facebook's social buttons every 24 hours. They do this to check for updated tags, and 24 hours is the longest duration possible. There are ways to have it scan quicker, but obviously, that's not what you're looking for.
For more information on how it scans, see:
developers.facebook.com/docs/reference/plugins/like/ (Search for "scrape"
So, if you have thousands of pages, that may just be a consequence of using Facebook on your pages, as Facebook will want to scan them. They should be spreading things out (and may with time), but there's no way to stop it.
One thing to check on your server is that the following file is hit-able. It will appear like a blank white page, and if you look at the source, it will load one Javascript file:
http://site.com/components/com_jfbconnect/assets/jfbcchannel.php
If that throws an error, you'll need to fix that. Let us know, and we can help.
Hope that at least explains,
Alex