It looks like a problem with mod_rewrite -- check your .htaccess file and make sure it has the `RewriteBase /` line in it.
Also, do you have any other .htaccess files in any parent directories that could be interfering?
If your .htaccess looks fine and you're still having problems, you can try disabling mod_rewrite in the config.php file.
Also, the version in SVN has a new fully-compatible version of the stopdesign theme checked-in (no changes needed). You might want to try that.