Is there anything you can think of that's different about the site where they don't work (upgrade rather than fresh install, in a subdirectory, extra contexts, etc.)?
You've probably tried these already, but:
- Manually delete all the files in the core/cache directory
- Clear the browser cacha *and cookies*
- Check the path in the modx_workspaces directory in PhpMyAdmin
- Make sure the filename is .htaccess, not ht.access
- Check the rewrite base line in .htacces
- Make sure mod_rewrite is enabled on the server
- Make sure you have this in all templates:
<base href="[[!++site_url]]" />